Starting phenix.real_space_refine on Sat Sep 12 19:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.map" model { file = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ogm_12884/09_2026/7ogm_12884.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 57 5.16 5 C 11029 2.51 5 N 3106 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17683 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 389 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 57} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 404 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "I" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 406 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 438 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 5, 'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "E" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 413 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 390 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "L" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4777 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 28, 'TRANS': 664} Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 38, 'ASP:plan': 21, 'PHE:plan': 4, 'ARG:plan': 15, 'ASN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 375 Chain: "N" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 4841 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 28, 'TRANS': 660} Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 14, 'GLU:plan': 33, 'ASP:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 281 Chain: "O" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4672 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 641 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 26, 'PHE:plan': 3, 'GLU:plan': 40, 'ARG:plan': 17, 'ASN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 406 Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 953 Classifications: {'RNAv2': 49} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 21, 'rna3p': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1, ' U%rna2p_pyr:plan': 2, ' A%rna3p_pur:plan': 4, ' A%rna3p_pur:plan2': 4, ' A%rna2p_pur:plan': 3, ' A%rna2p_pur:plan2': 3, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 3.90, per 1000 atoms: 0.22 Number of scatterers: 17683 At special positions: 0 Unit cell: (110.76, 109.695, 181.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 49 15.00 O 3442 8.00 N 3106 7.00 C 11029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 773.1 milliseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 25 sheets defined 34.0% alpha, 23.3% beta 8 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'K' and resid 7 through 18 Processing helix chain 'J' and resid 7 through 18 Processing helix chain 'I' and resid 7 through 19 removed outlier: 3.505A pdb=" N PHE I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'E' and resid 9 through 19 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 85 through 103 Proline residue: L 98 - end of helix Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 141 removed outlier: 4.498A pdb=" N VAL L 129 " --> pdb=" O ASN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 172 Processing helix chain 'L' and resid 197 through 212 removed outlier: 3.593A pdb=" N MET L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS L 209 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN L 212 " --> pdb=" O GLY L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 227 removed outlier: 3.624A pdb=" N GLU L 225 " --> pdb=" O GLU L 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY L 227 " --> pdb=" O VAL L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 removed outlier: 5.330A pdb=" N ALA L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG L 253 " --> pdb=" O LEU L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 280 Processing helix chain 'L' and resid 289 through 312 removed outlier: 3.699A pdb=" N ALA L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU L 310 " --> pdb=" O ARG L 306 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA L 311 " --> pdb=" O SER L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 388 Processing helix chain 'L' and resid 397 through 413 removed outlier: 4.117A pdb=" N ALA L 413 " --> pdb=" O ARG L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 454 removed outlier: 3.702A pdb=" N CYS L 444 " --> pdb=" O MET L 440 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 489 Processing helix chain 'L' and resid 515 through 530 removed outlier: 3.526A pdb=" N ALA L 522 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY L 528 " --> pdb=" O ASN L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 563 No H-bonds generated for 'chain 'L' and resid 561 through 563' Processing helix chain 'L' and resid 564 through 570 Processing helix chain 'L' and resid 573 through 584 Processing helix chain 'L' and resid 601 through 614 Processing helix chain 'L' and resid 650 through 655 Processing helix chain 'L' and resid 661 through 666 removed outlier: 3.718A pdb=" N LEU L 666 " --> pdb=" O THR L 663 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 693 No H-bonds generated for 'chain 'L' and resid 691 through 693' Processing helix chain 'N' and resid 67 through 71 Processing helix chain 'N' and resid 85 through 103 Proline residue: N 98 - end of helix Proline residue: N 101 - end of helix Processing helix chain 'N' and resid 125 through 141 removed outlier: 4.495A pdb=" N VAL N 129 " --> pdb=" O ASN N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 171 Processing helix chain 'N' and resid 197 through 212 removed outlier: 3.662A pdb=" N VAL N 206 " --> pdb=" O LEU N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 227 removed outlier: 3.557A pdb=" N ILE N 216 " --> pdb=" O GLN N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 242 through 258 removed outlier: 4.432A pdb=" N ALA N 252 " --> pdb=" O ALA N 248 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG N 253 " --> pdb=" O LEU N 249 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR N 258 " --> pdb=" O LEU N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 281 Processing helix chain 'N' and resid 290 through 312 Processing helix chain 'N' and resid 383 through 388 Processing helix chain 'N' and resid 397 through 413 removed outlier: 3.793A pdb=" N ALA N 413 " --> pdb=" O ARG N 409 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 454 removed outlier: 3.705A pdb=" N ALA N 441 " --> pdb=" O SER N 437 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 489 removed outlier: 4.465A pdb=" N HIS N 487 " --> pdb=" O ASP N 484 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 541 removed outlier: 3.642A pdb=" N VAL N 521 " --> pdb=" O GLU N 517 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY N 528 " --> pdb=" O ASN N 524 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL N 536 " --> pdb=" O HIS N 532 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN N 539 " --> pdb=" O GLY N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 563 No H-bonds generated for 'chain 'N' and resid 561 through 563' Processing helix chain 'N' and resid 564 through 570 Processing helix chain 'N' and resid 573 through 584 Processing helix chain 'N' and resid 601 through 614 Processing helix chain 'N' and resid 651 through 655 Processing helix chain 'N' and resid 661 through 665 Processing helix chain 'O' and resid 67 through 71 Processing helix chain 'O' and resid 85 through 100 removed outlier: 4.660A pdb=" N ILE O 91 " --> pdb=" O GLY O 87 " (cutoff:3.500A) Proline residue: O 98 - end of helix Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 125 through 141 removed outlier: 4.485A pdb=" N VAL O 129 " --> pdb=" O ASN O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 166 through 172 removed outlier: 3.992A pdb=" N GLU O 172 " --> pdb=" O ASP O 168 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 211 removed outlier: 3.642A pdb=" N VAL O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 227 removed outlier: 3.813A pdb=" N ILE O 216 " --> pdb=" O GLN O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 249 removed outlier: 3.925A pdb=" N ALA O 244 " --> pdb=" O GLU O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 260 removed outlier: 3.787A pdb=" N ILE O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 281 Processing helix chain 'O' and resid 292 through 312 Processing helix chain 'O' and resid 358 through 362 Processing helix chain 'O' and resid 383 through 388 Processing helix chain 'O' and resid 397 through 413 removed outlier: 3.762A pdb=" N ILE O 401 " --> pdb=" O LYS O 397 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY O 404 " --> pdb=" O GLU O 400 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA O 413 " --> pdb=" O ARG O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 438 through 453 Processing helix chain 'O' and resid 485 through 489 Processing helix chain 'O' and resid 515 through 541 removed outlier: 3.644A pdb=" N GLY O 528 " --> pdb=" O ASN O 524 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL O 536 " --> pdb=" O HIS O 532 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN O 539 " --> pdb=" O GLY O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 570 removed outlier: 3.605A pdb=" N ASP O 567 " --> pdb=" O ASP O 563 " (cutoff:3.500A) Processing helix chain 'O' and resid 573 through 584 Processing helix chain 'O' and resid 601 through 617 removed outlier: 3.723A pdb=" N ALA O 605 " --> pdb=" O ASP O 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 31 through 34 removed outlier: 6.809A pdb=" N SER K 23 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL K 62 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR K 25 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER K 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER J 38 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER J 23 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL J 62 " --> pdb=" O SER J 23 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR J 25 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 36 through 39 removed outlier: 6.882A pdb=" N LEU K 45 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE K 39 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER F 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 51 through 55 removed outlier: 6.336A pdb=" N LYS I 47 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE I 36 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER I 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 43 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE D 39 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU D 45 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 31 through 34 removed outlier: 3.697A pdb=" N GLY D 34 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER D 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE E 39 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 45 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER E 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR F 55 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN F 52 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 10 removed outlier: 3.818A pdb=" N THR L 20 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA L 39 " --> pdb=" O VAL L 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 150 through 154 removed outlier: 4.404A pdb=" N SER L 503 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA L 496 " --> pdb=" O SER L 503 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU L 505 " --> pdb=" O LYS L 494 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS L 494 " --> pdb=" O LEU L 505 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET L 507 " --> pdb=" O ASP L 492 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP L 492 " --> pdb=" O MET L 507 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE L 493 " --> pdb=" O MET L 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 327 through 328 removed outlier: 4.004A pdb=" N PHE L 343 " --> pdb=" O ALA L 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU L 433 " --> pdb=" O GLN L 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 327 through 328 removed outlier: 4.004A pdb=" N PHE L 343 " --> pdb=" O ALA L 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU L 433 " --> pdb=" O GLN L 349 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU L 377 " --> pdb=" O VAL L 427 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER L 429 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS L 379 " --> pdb=" O SER L 429 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE L 431 " --> pdb=" O HIS L 379 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN L 381 " --> pdb=" O ILE L 431 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU L 433 " --> pdb=" O ASN L 381 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 363 through 367 removed outlier: 3.726A pdb=" N GLU L 367 " --> pdb=" O GLY L 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 554 through 558 Processing sheet with id=AB2, first strand: chain 'L' and resid 625 through 628 removed outlier: 6.677A pdb=" N ARG L 686 " --> pdb=" O LEU L 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 632 through 633 removed outlier: 3.640A pdb=" N VAL L 639 " --> pdb=" O GLY L 647 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 17 through 20 removed outlier: 6.206A pdb=" N ALA N 39 " --> pdb=" O VAL N 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 160 through 163 removed outlier: 4.833A pdb=" N GLU N 192 " --> pdb=" O ASP N 176 " (cutoff:3.500A) removed outlier: 10.598A pdb=" N GLU N 190 " --> pdb=" O ASP N 508 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ASP N 508 " --> pdb=" O GLU N 190 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N GLU N 192 " --> pdb=" O GLN N 506 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLN N 506 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N GLN N 194 " --> pdb=" O ALA N 504 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ALA N 504 " --> pdb=" O GLN N 194 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 196 " --> pdb=" O ILE N 502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP N 492 " --> pdb=" O ASP N 508 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET N 491 " --> pdb=" O LEU N 468 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU N 468 " --> pdb=" O MET N 491 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE N 493 " --> pdb=" O MET N 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 329 through 331 removed outlier: 3.679A pdb=" N ARG N 330 " --> pdb=" O LEU N 342 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU N 351 " --> pdb=" O ILE N 431 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE N 431 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR N 353 " --> pdb=" O SER N 429 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER N 429 " --> pdb=" O THR N 353 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR N 355 " --> pdb=" O VAL N 427 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL N 427 " --> pdb=" O THR N 355 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY N 357 " --> pdb=" O VAL N 425 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL N 425 " --> pdb=" O GLY N 357 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU N 377 " --> pdb=" O VAL N 427 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER N 429 " --> pdb=" O LEU N 377 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N HIS N 379 " --> pdb=" O SER N 429 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE N 431 " --> pdb=" O HIS N 379 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN N 381 " --> pdb=" O ILE N 431 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLU N 433 " --> pdb=" O ASN N 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 363 through 366 Processing sheet with id=AB8, first strand: chain 'N' and resid 554 through 559 Processing sheet with id=AB9, first strand: chain 'N' and resid 629 through 633 removed outlier: 3.511A pdb=" N GLY N 636 " --> pdb=" O VAL N 633 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.552A pdb=" N TYR O 11 " --> pdb=" O HIS O 14 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET O 35 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA O 39 " --> pdb=" O VAL O 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 160 through 163 removed outlier: 4.255A pdb=" N SER O 503 " --> pdb=" O ALA O 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET O 491 " --> pdb=" O LEU O 468 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE O 493 " --> pdb=" O MET O 466 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA O 462 " --> pdb=" O GLY O 497 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 327 through 331 removed outlier: 3.687A pdb=" N ARG O 330 " --> pdb=" O LEU O 342 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 327 through 331 removed outlier: 3.687A pdb=" N ARG O 330 " --> pdb=" O LEU O 342 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU O 377 " --> pdb=" O VAL O 427 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER O 429 " --> pdb=" O LEU O 377 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS O 379 " --> pdb=" O SER O 429 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 554 through 559 Processing sheet with id=AC6, first strand: chain 'O' and resid 637 through 639 Processing sheet with id=AC7, first strand: chain 'O' and resid 674 through 675 890 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2839 1.28 - 1.42: 4194 1.42 - 1.55: 10792 1.55 - 1.69: 103 1.69 - 1.83: 111 Bond restraints: 18039 Sorted by residual: bond pdb=" C THR O 38 " pdb=" O THR O 38 " ideal model delta sigma weight residual 1.234 1.142 0.092 1.20e-02 6.94e+03 5.84e+01 bond pdb=" C ASN O 164 " pdb=" O ASN O 164 " ideal model delta sigma weight residual 1.238 1.144 0.094 1.28e-02 6.10e+03 5.38e+01 bond pdb=" C LEU D 45 " pdb=" O LEU D 45 " ideal model delta sigma weight residual 1.236 1.153 0.082 1.21e-02 6.83e+03 4.65e+01 bond pdb=" C ARG L 330 " pdb=" O ARG L 330 " ideal model delta sigma weight residual 1.234 1.153 0.081 1.20e-02 6.94e+03 4.55e+01 bond pdb=" C LEU L 18 " pdb=" O LEU L 18 " ideal model delta sigma weight residual 1.233 1.156 0.077 1.28e-02 6.10e+03 3.61e+01 ... (remaining 18034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 19853 2.30 - 4.60: 4617 4.60 - 6.90: 385 6.90 - 9.20: 49 9.20 - 11.50: 15 Bond angle restraints: 24919 Sorted by residual: angle pdb=" CA PHE L 9 " pdb=" C PHE L 9 " pdb=" O PHE L 9 " ideal model delta sigma weight residual 121.58 112.17 9.41 1.16e+00 7.43e-01 6.58e+01 angle pdb=" CA PHE L 9 " pdb=" CB PHE L 9 " pdb=" CG PHE L 9 " ideal model delta sigma weight residual 113.80 121.63 -7.83 1.00e+00 1.00e+00 6.14e+01 angle pdb=" CA ILE L 5 " pdb=" C ILE L 5 " pdb=" O ILE L 5 " ideal model delta sigma weight residual 121.67 113.46 8.21 1.06e+00 8.90e-01 5.99e+01 angle pdb=" C ARG O 7 " pdb=" N LYS O 8 " pdb=" CA LYS O 8 " ideal model delta sigma weight residual 122.67 111.85 10.82 1.47e+00 4.63e-01 5.42e+01 angle pdb=" N ASP N 490 " pdb=" CA ASP N 490 " pdb=" C ASP N 490 " ideal model delta sigma weight residual 113.23 104.35 8.88 1.24e+00 6.50e-01 5.13e+01 ... (remaining 24914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 10261 33.43 - 66.86: 390 66.86 - 100.29: 54 100.29 - 133.72: 0 133.72 - 167.16: 1 Dihedral angle restraints: 10706 sinusoidal: 3705 harmonic: 7001 Sorted by residual: dihedral pdb=" C4' U P 21 " pdb=" C3' U P 21 " pdb=" C2' U P 21 " pdb=" C1' U P 21 " ideal model delta sinusoidal sigma weight residual 36.34 -44.60 80.94 1 3.10e+00 1.04e-01 8.42e+02 dihedral pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " pdb=" C1' U P 20 " ideal model delta sinusoidal sigma weight residual 36.34 -41.09 77.44 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' A P 3 " pdb=" C3' A P 3 " pdb=" C2' A P 3 " pdb=" C1' A P 3 " ideal model delta sinusoidal sigma weight residual 36.35 -39.72 76.06 1 3.10e+00 1.04e-01 7.58e+02 ... (remaining 10703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2689 0.153 - 0.305: 498 0.305 - 0.458: 16 0.458 - 0.611: 3 0.611 - 0.764: 1 Chirality restraints: 3207 Sorted by residual: chirality pdb=" P A P 1 " pdb=" OP1 A P 1 " pdb=" OP2 A P 1 " pdb=" O5' A P 1 " both_signs ideal model delta sigma weight residual True 2.17 2.94 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CB VAL L 162 " pdb=" CA VAL L 162 " pdb=" CG1 VAL L 162 " pdb=" CG2 VAL L 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA THR L 331 " pdb=" N THR L 331 " pdb=" C THR L 331 " pdb=" CB THR L 331 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 3204 not shown) Planarity restraints: 3065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 39 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C PHE D 39 " 0.095 2.00e-02 2.50e+03 pdb=" O PHE D 39 " -0.037 2.00e-02 2.50e+03 pdb=" N ASP D 40 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 145 " -0.055 2.00e-02 2.50e+03 3.50e-02 2.14e+01 pdb=" CG PHE L 145 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE L 145 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE L 145 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE L 145 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE L 145 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE L 145 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 230 " 0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C ARG O 230 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG O 230 " 0.028 2.00e-02 2.50e+03 pdb=" N TRP O 231 " 0.026 2.00e-02 2.50e+03 ... (remaining 3062 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1613 2.78 - 3.31: 17943 3.31 - 3.84: 26261 3.84 - 4.37: 33563 4.37 - 4.90: 54029 Nonbonded interactions: 133409 Sorted by model distance: nonbonded pdb=" CG2 ILE N 555 " pdb=" CE LYS N 596 " model vdw 2.245 3.860 nonbonded pdb=" N ILE L 5 " pdb=" O ILE L 5 " model vdw 2.256 2.496 nonbonded pdb=" OD1 ASP N 55 " pdb=" N PHE N 56 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR O 380 " pdb=" OG SER O 438 " model vdw 2.275 3.040 nonbonded pdb=" O ASP O 159 " pdb=" NE2 GLN O 160 " model vdw 2.280 3.120 ... (remaining 133404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 9 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 17 or (resid 18 through 19 and (nam \ e N or name CA or name C or name O or name CB )) or resid 20 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 throug \ h 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or re \ sid 43 through 44 or (resid 45 through 48 and (name N or name CA or name C or na \ me O or name CB )) or resid 49 through 54 or (resid 55 through 58 and (name N or \ name CA or name C or name O or name CB )) or resid 59 through 67 or (resid 68 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 9 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 through 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 24 or (resid 25 and (n \ ame N or name CA or name C or name O or name CB )) or resid 26 through 34 or (re \ sid 35 and (name N or name CA or name C or name O or name CB )) or resid 36 thro \ ugh 38 or (resid 39 through 42 and (name N or name CA or name C or name O or nam \ e CB )) or resid 43 through 44 or (resid 45 through 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 54 or (resid 55 through 58 a \ nd (name N or name CA or name C or name O or name CB )) or resid 59 through 68)) \ selection = (chain 'F' and (resid 9 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 44 or (resid 45 through 48 and (nam \ e N or name CA or name C or name O or name CB )) or resid 49 through 54 or (resi \ d 55 through 58 and (name N or name CA or name C or name O or name CB )) or resi \ d 59 through 67 or (resid 68 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'I' and (resid 9 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 27 or (resid 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 41 or (resid 42 and (n \ ame N or name CA or name C or name O or name CB )) or resid 43 through 44 or (re \ sid 45 through 48 and (name N or name CA or name C or name O or name CB )) or re \ sid 49 through 56 or (resid 57 through 58 and (name N or name CA or name C or na \ me O or name CB )) or resid 59 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'J' and (resid 9 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 54 or (resid 55 throug \ h 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 67 or (resid 68 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 41 or (resid 42 and (n \ ame N or name CA or name C or name O or name CB )) or resid 43 through 44 or (re \ sid 45 through 48 and (name N or name CA or name C or name O or name CB )) or re \ sid 49 through 67 or (resid 68 and (name N or name CA or name C or name O or nam \ e CB )))) } ncs_group { reference = (chain 'L' and (resid 1 through 47 or (resid 48 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 109 or ( \ resid 110 and (name N or name CA or name C or name O or name CB )) or resid 111 \ through 158 or (resid 159 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 167 or (resid 168 through 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 17 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 173 or (resi \ d 174 and (name N or name CA or name C or name O or name CB )) or resid 175 thro \ ugh 182 or (resid 183 through 185 and (name N or name CA or name C or name O or \ name CB )) or resid 186 through 197 or (resid 198 and (name N or name CA or name \ C or name O or name CB )) or resid 199 through 223 or (resid 224 and (name N or \ name CA or name C or name O or name CB )) or resid 225 through 237 or (resid 23 \ 8 through 241 and (name N or name CA or name C or name O or name CB )) or resid \ 242 through 263 or (resid 264 through 266 and (name N or name CA or name C or na \ me O or name CB )) or resid 267 through 277 or (resid 278 through 279 and (name \ N or name CA or name C or name O or name CB )) or resid 280 or (resid 281 throug \ h 286 and (name N or name CA or name C or name O or name CB )) or resid 287 thro \ ugh 360 or (resid 361 through 363 and (name N or name CA or name C or name O or \ name CB )) or resid 364 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 416 or (resid 417 through 420 an \ d (name N or name CA or name C or name O or name CB )) or resid 421 through 457 \ or (resid 458 through 460 and (name N or name CA or name C or name O or name CB \ )) or resid 461 through 469 or (resid 470 through 471 and (name N or name CA or \ name C or name O or name CB )) or resid 472 through 484 or (resid 485 and (name \ N or name CA or name C or name O or name CB )) or resid 486 through 489 or (resi \ d 490 and (name N or name CA or name C or name O or name CB )) or resid 491 thro \ ugh 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) o \ r resid 501 through 509 or (resid 510 and (name N or name CA or name C or name O \ or name CB )) or resid 511 through 516 or (resid 517 and (name N or name CA or \ name C or name O or name CB )) or resid 518 through 519 or (resid 520 and (name \ N or name CA or name C or name O or name CB )) or resid 521 through 557 or (resi \ d 558 through 561 and (name N or name CA or name C or name O or name CB )) or re \ sid 562 through 564 or (resid 565 through 569 and (name N or name CA or name C o \ r name O or name CB )) or resid 570 through 575 or (resid 576 through 579 and (n \ ame N or name CA or name C or name O or name CB )) or resid 580 through 588 or ( \ resid 589 through 592 and (name N or name CA or name C or name O or name CB )) o \ r resid 593 through 600 or (resid 601 and (name N or name CA or name C or name O \ or name CB )) or (resid 602 through 608 and (name N or name CA or name C or nam \ e O or name CB )) or resid 609 through 611 or (resid 612 through 615 and (name N \ or name CA or name C or name O or name CB )) or resid 616 through 620 or (resid \ 621 and (name N or name CA or name C or name O or name CB )) or (resid 622 thro \ ugh 626 and (name N or name CA or name C or name O or name CB )) or (resid 627 t \ hrough 635 and (name N or name CA or name C or name O or name CB )) or resid 636 \ through 640 or (resid 641 and (name N or name CA or name C or name O or name CB \ )) or (resid 642 through 650 and (name N or name CA or name C or name O or name \ CB )) or resid 651 through 653 or (resid 654 through 668 and (name N or name CA \ or name C or name O or name CB )) or (resid 669 through 672 and (name N or name \ CA or name C or name O or name CB )) or resid 673 or (resid 674 through 682 and \ (name N or name CA or name C or name O or name CB )) or resid 683 or (resid 684 \ through 687 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 88 or (resid 689 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 18 or (resid 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 76 or (res \ id 77 through 79 and (name N or name CA or name C or name O or name CB )) or res \ id 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or r \ esid 82 through 158 or (resid 159 through 160 and (name N or name CA or name C o \ r name O or name CB )) or resid 161 through 197 or (resid 198 and (name N or nam \ e CA or name C or name O or name CB )) or resid 199 through 237 or (resid 238 th \ rough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 \ or (resid 243 through 245 and (name N or name CA or name C or name O or name CB \ )) or resid 246 through 255 or (resid 256 through 257 and (name N or name CA or \ name C or name O or name CB )) or resid 258 or (resid 259 and (name N or name CA \ or name C or name O or name CB )) or resid 260 through 261 or (resid 262 throug \ h 266 and (name N or name CA or name C or name O or name CB )) or resid 267 thro \ ugh 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) o \ r resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 277 or (resid 278 through 279 and (name N or name CA or \ name C or name O or name CB )) or resid 280 or (resid 281 through 286 and (name \ N or name CA or name C or name O or name CB )) or resid 287 through 290 or (resi \ d 291 through 292 and (name N or name CA or name C or name O or name CB )) or re \ sid 293 through 297 or (resid 298 through 299 and (name N or name CA or name C o \ r name O or name CB )) or resid 300 or (resid 301 through 302 and (name N or nam \ e CA or name C or name O or name CB )) or resid 303 through 320 or (resid 321 an \ d (name N or name CA or name C or name O or name CB )) or resid 322 or (resid 32 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 324 through \ 327 or (resid 328 and (name N or name CA or name C or name O or name CB )) or re \ sid 329 through 360 or (resid 361 through 363 and (name N or name CA or name C o \ r name O or name CB )) or resid 364 through 365 or (resid 366 through 367 and (n \ ame N or name CA or name C or name O or name CB )) or resid 368 through 371 or ( \ resid 372 and (name N or name CA or name C or name O or name CB )) or resid 373 \ through 388 or (resid 389 and (name N or name CA or name C or name O or name CB \ )) or resid 390 through 391 or (resid 392 and (name N or name CA or name C or na \ me O or name CB )) or resid 393 through 416 or (resid 417 through 420 and (name \ N or name CA or name C or name O or name CB )) or resid 421 through 457 or (resi \ d 458 through 460 and (name N or name CA or name C or name O or name CB )) or re \ sid 461 through 469 or (resid 470 through 471 and (name N or name CA or name C o \ r name O or name CB )) or resid 472 or (resid 473 and (name N or name CA or name \ C or name O or name CB )) or resid 474 through 483 or (resid 484 through 485 an \ d (name N or name CA or name C or name O or name CB )) or resid 486 through 489 \ or (resid 490 and (name N or name CA or name C or name O or name CB )) or resid \ 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or re \ sid 493 through 499 or (resid 500 and (name N or name CA or name C or name O or \ name CB )) or resid 501 through 509 or (resid 510 and (name N or name CA or name \ C or name O or name CB )) or resid 511 or (resid 512 and (name N or name CA or \ name C or name O or name CB )) or resid 513 through 515 or (resid 516 through 51 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 518 through \ 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) or re \ sid 521 through 526 or (resid 527 and (name N or name CA or name C or name O or \ name CB )) or resid 528 through 537 or (resid 538 and (name N or name CA or name \ C or name O or name CB )) or resid 539 through 546 or (resid 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 through 549 or (resid 55 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 551 through \ 557 or (resid 558 through 561 and (name N or name CA or name C or name O or name \ CB )) or resid 562 through 570 or (resid 571 and (name N or name CA or name C o \ r name O or name CB )) or resid 572 through 575 or (resid 576 through 579 and (n \ ame N or name CA or name C or name O or name CB )) or resid 580 through 588 or ( \ resid 589 through 592 and (name N or name CA or name C or name O or name CB )) o \ r resid 593 through 595 or (resid 596 and (name N or name CA or name C or name O \ or name CB )) or resid 597 through 603 or (resid 604 through 608 and (name N or \ name CA or name C or name O or name CB )) or resid 609 or (resid 610 through 61 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 616 through \ 620 or (resid 621 and (name N or name CA or name C or name O or name CB )) or (r \ esid 622 through 626 and (name N or name CA or name C or name O or name CB )) or \ resid 627 or (resid 628 through 635 and (name N or name CA or name C or name O \ or name CB )) or resid 636 through 648 or (resid 649 through 650 and (name N or \ name CA or name C or name O or name CB )) or resid 651 through 653 or (resid 654 \ through 668 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 69 through 681 or (resid 682 and (name N or name CA or name C or name O or name \ CB )) or (resid 683 through 687 and (name N or name CA or name C or name O or na \ me CB )) or resid 688 or (resid 689 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'O' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 18 or (resid 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 47 or (resid 48 through \ 51 and (name N or name CA or name C or name O or name CB )) or resid 52 through \ 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or res \ id 80 through 109 or (resid 110 and (name N or name CA or name C or name O or na \ me CB )) or resid 111 through 159 or (resid 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 173 or (resid 174 \ and (name N or name CA or name C or name O or name CB )) or resid 175 through 18 \ 2 or (resid 183 through 185 and (name N or name CA or name C or name O or name C \ B )) or resid 186 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 242 or (resid 243 through 245 and (nam \ e N or name CA or name C or name O or name CB )) or resid 246 through 268 or (re \ sid 269 and (name N or name CA or name C or name O or name CB )) or resid 270 th \ rough 297 or (resid 298 through 299 and (name N or name CA or name C or name O o \ r name CB )) or resid 300 or (resid 301 through 302 and (name N or name CA or na \ me C or name O or name CB )) or resid 303 through 320 or (resid 321 and (name N \ or name CA or name C or name O or name CB )) or resid 322 through 327 or (resid \ 328 and (name N or name CA or name C or name O or name CB )) or resid 329 throug \ h 346 or (resid 347 and (name N or name CA or name C or name O or name CB )) or \ resid 348 through 362 or (resid 363 and (name N or name CA or name C or name O o \ r name CB )) or resid 364 through 365 or (resid 366 through 367 and (name N or n \ ame CA or name C or name O or name CB )) or resid 368 through 370 or (resid 371 \ through 372 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 3 through 398 or (resid 399 through 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 515 or (resid 516 through 517 and (name N \ or name CA or name C or name O or name CB )) or resid 518 through 526 or (resid \ 527 and (name N or name CA or name C or name O or name CB )) or resid 528 throug \ h 634 or (resid 635 and (name N or name CA or name C or name O or name CB )) or \ resid 636 through 689)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.050 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.015 0.094 18039 Z= 1.149 Angle : 1.858 11.501 24919 Z= 1.340 Chirality : 0.113 0.764 3207 Planarity : 0.010 0.055 3065 Dihedral : 17.403 167.155 6194 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 9.03 % Favored : 87.85 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2436 helix: -0.70 (0.18), residues: 723 sheet: -0.14 (0.21), residues: 532 loop : -1.02 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG L 100 TYR 0.042 0.008 TYR N 11 PHE 0.065 0.010 PHE L 145 TRP 0.054 0.011 TRP N 233 HIS 0.039 0.008 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.01500 / 1.15 (18039) covalent geometry : angle 1.85838 / 1.34 (24919) hydrogen bonds : bond 0.20355 / 14.37 ( 897) hydrogen bonds : angle 7.66259 / 5.52 ( 2450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 42 PHE cc_start: 0.7779 (m-80) cc_final: 0.7405 (m-10) REVERT: I 25 TYR cc_start: 0.8408 (m-80) cc_final: 0.8206 (m-80) REVERT: I 42 PHE cc_start: 0.7151 (m-80) cc_final: 0.6866 (p90) REVERT: E 32 LEU cc_start: 0.8767 (mt) cc_final: 0.8467 (mp) REVERT: F 27 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8888 (m) REVERT: L 169 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: L 202 LEU cc_start: 0.8356 (tp) cc_final: 0.7986 (tt) REVERT: L 260 ILE cc_start: 0.9280 (mm) cc_final: 0.8887 (tt) REVERT: L 281 LEU cc_start: 0.7587 (mm) cc_final: 0.7286 (pp) REVERT: L 287 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6375 (p) REVERT: L 494 LYS cc_start: 0.8987 (mttt) cc_final: 0.8600 (mttp) REVERT: N 9 PHE cc_start: 0.8397 (m-10) cc_final: 0.8172 (m-80) REVERT: N 88 GLU cc_start: 0.8284 (mp0) cc_final: 0.7909 (mt-10) REVERT: N 433 GLU cc_start: 0.6705 (pt0) cc_final: 0.6481 (pt0) REVERT: N 466 MET cc_start: 0.8426 (mmm) cc_final: 0.8032 (mmt) REVERT: O 88 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8143 (mt-10) REVERT: O 174 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7840 (mtpt) REVERT: O 597 ILE cc_start: 0.8577 (mp) cc_final: 0.8076 (tt) outliers start: 47 outliers final: 5 residues processed: 345 average time/residue: 0.1306 time to fit residues: 69.5091 Evaluate side-chains 196 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain L residue 169 GLU Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 287 THR Chi-restraints excluded: chain L residue 342 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 GLN L 218 ASN L 264 GLN L 520 GLN L 532 HIS N 109 ASN N 291 ASN N 487 HIS O 26 GLN O 64 GLN O 218 ASN O 298 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098286 restraints weight = 32063.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093865 restraints weight = 24191.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095197 restraints weight = 25455.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095322 restraints weight = 17648.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096273 restraints weight = 15345.610| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18039 Z= 0.177 Angle : 0.988 19.370 24919 Z= 0.455 Chirality : 0.087 2.178 3207 Planarity : 0.005 0.046 3065 Dihedral : 12.760 163.662 3157 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.66 % Allowed : 16.00 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2436 helix: 1.31 (0.19), residues: 729 sheet: -0.02 (0.21), residues: 604 loop : -0.64 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 409 TYR 0.016 0.002 TYR J 25 PHE 0.022 0.002 PHE N 493 TRP 0.020 0.002 TRP O 231 HIS 0.007 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (18039) covalent geometry : angle 0.98823 / 0.45 (24919) hydrogen bonds : bond 0.05306 / 3.82 ( 897) hydrogen bonds : angle 5.28281 / 3.77 ( 2450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: I 25 TYR cc_start: 0.8605 (m-80) cc_final: 0.8371 (m-80) REVERT: I 42 PHE cc_start: 0.6360 (m-80) cc_final: 0.5996 (p90) REVERT: D 45 LEU cc_start: 0.8623 (tt) cc_final: 0.8378 (mm) REVERT: D 59 ILE cc_start: 0.8066 (tp) cc_final: 0.7843 (tp) REVERT: F 26 LEU cc_start: 0.8339 (mm) cc_final: 0.8123 (mm) REVERT: L 281 LEU cc_start: 0.7801 (mm) cc_final: 0.7452 (tp) REVERT: L 494 LYS cc_start: 0.8999 (mttt) cc_final: 0.8718 (mttp) REVERT: L 686 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.6213 (mpt180) REVERT: N 138 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8945 (mp) REVERT: N 433 GLU cc_start: 0.6978 (pt0) cc_final: 0.6768 (pt0) REVERT: N 507 MET cc_start: 0.7125 (mtp) cc_final: 0.6751 (ttm) REVERT: N 571 LYS cc_start: 0.7938 (tptt) cc_final: 0.7497 (tppt) REVERT: O 90 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8771 (tm) outliers start: 40 outliers final: 17 residues processed: 235 average time/residue: 0.1069 time to fit residues: 41.8232 Evaluate side-chains 190 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 191 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 242 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 201 optimal weight: 0.0040 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 243 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** N 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 487 HIS O 487 HIS O 556 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.138998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090917 restraints weight = 32720.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087100 restraints weight = 24238.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087863 restraints weight = 22364.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088250 restraints weight = 17180.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088579 restraints weight = 15432.448| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 18039 Z= 0.315 Angle : 0.911 18.206 24919 Z= 0.440 Chirality : 0.075 2.230 3207 Planarity : 0.006 0.051 3065 Dihedral : 12.924 168.803 3146 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.44 % Allowed : 16.27 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2436 helix: 1.32 (0.19), residues: 727 sheet: -0.26 (0.22), residues: 610 loop : -0.74 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 153 TYR 0.023 0.003 TYR E 55 PHE 0.026 0.002 PHE L 145 TRP 0.026 0.003 TRP O 231 HIS 0.014 0.002 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.32 (18039) covalent geometry : angle 0.91104 / 0.44 (24919) hydrogen bonds : bond 0.05794 / 4.14 ( 897) hydrogen bonds : angle 5.17008 / 3.67 ( 2450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 28 ASN cc_start: 0.7924 (t0) cc_final: 0.7687 (p0) REVERT: K 32 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8554 (mt) REVERT: J 55 TYR cc_start: 0.7321 (m-80) cc_final: 0.6872 (m-80) REVERT: I 25 TYR cc_start: 0.8640 (m-80) cc_final: 0.8424 (m-80) REVERT: I 42 PHE cc_start: 0.6603 (m-80) cc_final: 0.6071 (p90) REVERT: D 45 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8218 (mm) REVERT: L 281 LEU cc_start: 0.7688 (mm) cc_final: 0.7467 (tp) REVERT: L 297 LEU cc_start: 0.8928 (pp) cc_final: 0.8715 (tt) REVERT: L 494 LYS cc_start: 0.9052 (mttt) cc_final: 0.8712 (mttp) REVERT: N 138 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9006 (mp) REVERT: N 433 GLU cc_start: 0.7064 (pt0) cc_final: 0.6743 (tt0) REVERT: N 480 ASP cc_start: 0.8280 (t0) cc_final: 0.8032 (t70) REVERT: N 537 MET cc_start: 0.8164 (mtp) cc_final: 0.7885 (mtp) REVERT: N 571 LYS cc_start: 0.8022 (tptt) cc_final: 0.7687 (tppt) REVERT: O 42 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8968 (m) REVERT: O 90 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8924 (tm) REVERT: O 176 ASP cc_start: 0.8007 (t0) cc_final: 0.7793 (t0) outliers start: 82 outliers final: 48 residues processed: 247 average time/residue: 0.1023 time to fit residues: 42.6229 Evaluate side-chains 218 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 411 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 461 VAL Chi-restraints excluded: chain N residue 502 ILE Chi-restraints excluded: chain N residue 503 SER Chi-restraints excluded: chain N residue 576 ILE Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 476 VAL Chi-restraints excluded: chain O residue 495 VAL Chi-restraints excluded: chain O residue 556 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 11 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 238 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.143141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097619 restraints weight = 32649.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092036 restraints weight = 27011.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093887 restraints weight = 25152.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093713 restraints weight = 18385.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094267 restraints weight = 15794.051| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18039 Z= 0.128 Angle : 0.742 17.734 24919 Z= 0.346 Chirality : 0.067 2.094 3207 Planarity : 0.004 0.046 3065 Dihedral : 12.649 174.427 3146 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.78 % Allowed : 18.53 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2436 helix: 1.78 (0.19), residues: 738 sheet: 0.06 (0.22), residues: 611 loop : -0.59 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 409 TYR 0.015 0.002 TYR E 55 PHE 0.014 0.001 PHE N 493 TRP 0.018 0.001 TRP O 231 HIS 0.030 0.001 HIS O 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (18039) covalent geometry : angle 0.74199 / 0.35 (24919) hydrogen bonds : bond 0.03974 / 2.88 ( 897) hydrogen bonds : angle 4.68615 / 3.34 ( 2450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 32 LEU cc_start: 0.8689 (mt) cc_final: 0.8375 (mt) REVERT: K 42 PHE cc_start: 0.7428 (p90) cc_final: 0.7126 (p90) REVERT: J 55 TYR cc_start: 0.7258 (m-80) cc_final: 0.6829 (m-80) REVERT: I 42 PHE cc_start: 0.6511 (m-80) cc_final: 0.6022 (p90) REVERT: D 45 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8083 (mm) REVERT: E 46 LEU cc_start: 0.8238 (tt) cc_final: 0.8034 (tt) REVERT: L 494 LYS cc_start: 0.8949 (mttt) cc_final: 0.8649 (mttp) REVERT: N 138 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8946 (mp) REVERT: N 433 GLU cc_start: 0.6888 (pt0) cc_final: 0.6663 (tt0) REVERT: N 507 MET cc_start: 0.7172 (mtp) cc_final: 0.6968 (ttm) REVERT: N 571 LYS cc_start: 0.7874 (tptt) cc_final: 0.7580 (tppt) REVERT: O 176 ASP cc_start: 0.7968 (t0) cc_final: 0.7735 (t0) REVERT: O 425 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8896 (p) outliers start: 57 outliers final: 32 residues processed: 224 average time/residue: 0.1010 time to fit residues: 38.0882 Evaluate side-chains 201 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 390 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 576 ILE Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 495 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 212 optimal weight: 0.0670 chunk 205 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.143300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098083 restraints weight = 32435.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092073 restraints weight = 26942.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093380 restraints weight = 24825.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094071 restraints weight = 17189.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094226 restraints weight = 15239.871| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18039 Z= 0.126 Angle : 0.720 18.300 24919 Z= 0.331 Chirality : 0.064 2.023 3207 Planarity : 0.004 0.046 3065 Dihedral : 12.557 179.383 3146 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.05 % Allowed : 19.39 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2436 helix: 1.86 (0.19), residues: 738 sheet: 0.07 (0.22), residues: 622 loop : -0.44 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 409 TYR 0.012 0.002 TYR L 267 PHE 0.014 0.001 PHE O 207 TRP 0.017 0.001 TRP O 231 HIS 0.006 0.001 HIS O 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (18039) covalent geometry : angle 0.71974 / 0.33 (24919) hydrogen bonds : bond 0.03722 / 2.67 ( 897) hydrogen bonds : angle 4.49000 / 3.20 ( 2450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: K 32 LEU cc_start: 0.8705 (mt) cc_final: 0.8354 (mt) REVERT: K 42 PHE cc_start: 0.7433 (p90) cc_final: 0.7125 (p90) REVERT: J 55 TYR cc_start: 0.7344 (m-80) cc_final: 0.6874 (m-80) REVERT: I 42 PHE cc_start: 0.6530 (m-80) cc_final: 0.6136 (p90) REVERT: D 45 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8069 (mm) REVERT: L 494 LYS cc_start: 0.8949 (mttt) cc_final: 0.8663 (mttp) REVERT: N 138 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8924 (mp) REVERT: N 433 GLU cc_start: 0.6850 (pt0) cc_final: 0.6596 (tt0) REVERT: N 507 MET cc_start: 0.7277 (mtp) cc_final: 0.6989 (ttm) REVERT: N 571 LYS cc_start: 0.7881 (tptt) cc_final: 0.7538 (tppt) REVERT: O 425 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8899 (p) outliers start: 61 outliers final: 36 residues processed: 230 average time/residue: 0.1092 time to fit residues: 42.1180 Evaluate side-chains 205 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 390 THR Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 576 ILE Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 448 LEU Chi-restraints excluded: chain O residue 495 VAL Chi-restraints excluded: chain O residue 556 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 82 optimal weight: 6.9990 chunk 238 optimal weight: 0.0030 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 overall best weight: 1.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094083 restraints weight = 32402.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091817 restraints weight = 24604.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093180 restraints weight = 21042.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093094 restraints weight = 16692.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093294 restraints weight = 14443.179| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18039 Z= 0.174 Angle : 0.718 18.733 24919 Z= 0.337 Chirality : 0.063 1.975 3207 Planarity : 0.004 0.047 3065 Dihedral : 12.480 178.716 3146 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.92 % Allowed : 20.19 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2436 helix: 1.88 (0.20), residues: 738 sheet: -0.01 (0.22), residues: 634 loop : -0.45 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 409 TYR 0.043 0.002 TYR L 267 PHE 0.025 0.002 PHE N 9 TRP 0.018 0.001 TRP O 231 HIS 0.028 0.002 HIS O 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (18039) covalent geometry : angle 0.71791 / 0.34 (24919) hydrogen bonds : bond 0.04030 / 2.87 ( 897) hydrogen bonds : angle 4.49363 / 3.20 ( 2450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: K 32 LEU cc_start: 0.8572 (mt) cc_final: 0.8300 (mt) REVERT: K 42 PHE cc_start: 0.7257 (p90) cc_final: 0.6969 (p90) REVERT: J 55 TYR cc_start: 0.7100 (m-80) cc_final: 0.6784 (m-80) REVERT: I 42 PHE cc_start: 0.6361 (m-80) cc_final: 0.5941 (p90) REVERT: D 45 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7825 (mm) REVERT: L 369 MET cc_start: 0.8903 (mmm) cc_final: 0.8698 (mmt) REVERT: L 429 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8652 (t) REVERT: L 494 LYS cc_start: 0.8839 (mttt) cc_final: 0.8505 (mttp) REVERT: N 138 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8931 (mp) REVERT: N 433 GLU cc_start: 0.6835 (pt0) cc_final: 0.6546 (tt0) REVERT: N 507 MET cc_start: 0.7250 (mtp) cc_final: 0.6932 (ttm) REVERT: N 571 LYS cc_start: 0.7751 (tptt) cc_final: 0.7302 (tppt) REVERT: O 176 ASP cc_start: 0.7940 (t0) cc_final: 0.7660 (t0) outliers start: 59 outliers final: 41 residues processed: 211 average time/residue: 0.1098 time to fit residues: 39.3389 Evaluate side-chains 206 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 429 SER Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 390 THR Chi-restraints excluded: chain N residue 411 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 448 LEU Chi-restraints excluded: chain O residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 106 optimal weight: 4.9990 chunk 241 optimal weight: 40.0000 chunk 20 optimal weight: 50.0000 chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 140 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 174 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 234 optimal weight: 40.0000 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 218 ASN N 379 HIS O 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.143941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096185 restraints weight = 32661.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093749 restraints weight = 24441.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094942 restraints weight = 19216.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095161 restraints weight = 14777.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095274 restraints weight = 13641.614| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18039 Z= 0.112 Angle : 0.675 18.991 24919 Z= 0.312 Chirality : 0.061 1.902 3207 Planarity : 0.004 0.045 3065 Dihedral : 12.260 177.654 3146 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.52 % Allowed : 19.65 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2436 helix: 2.11 (0.20), residues: 730 sheet: 0.11 (0.22), residues: 629 loop : -0.41 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 409 TYR 0.040 0.002 TYR L 267 PHE 0.018 0.001 PHE N 9 TRP 0.016 0.001 TRP O 231 HIS 0.010 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18039) covalent geometry : angle 0.67530 / 0.31 (24919) hydrogen bonds : bond 0.03356 / 2.41 ( 897) hydrogen bonds : angle 4.32466 / 3.08 ( 2450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: K 32 LEU cc_start: 0.8713 (mt) cc_final: 0.8187 (mt) REVERT: K 42 PHE cc_start: 0.7287 (p90) cc_final: 0.6939 (p90) REVERT: J 55 TYR cc_start: 0.7426 (m-80) cc_final: 0.7117 (m-80) REVERT: I 42 PHE cc_start: 0.6488 (m-80) cc_final: 0.6032 (p90) REVERT: D 45 LEU cc_start: 0.8162 (tt) cc_final: 0.7880 (mm) REVERT: L 369 MET cc_start: 0.8934 (mmm) cc_final: 0.8718 (mmt) REVERT: L 429 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8679 (t) REVERT: L 494 LYS cc_start: 0.8845 (mttt) cc_final: 0.8568 (mttp) REVERT: N 138 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8691 (mm) REVERT: N 433 GLU cc_start: 0.6773 (pt0) cc_final: 0.6482 (tt0) REVERT: N 507 MET cc_start: 0.7101 (mtp) cc_final: 0.6888 (ttm) REVERT: N 571 LYS cc_start: 0.7846 (tptt) cc_final: 0.7413 (tppt) REVERT: O 62 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7759 (p0) REVERT: O 176 ASP cc_start: 0.7955 (t0) cc_final: 0.7603 (t0) REVERT: O 425 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8894 (p) outliers start: 53 outliers final: 37 residues processed: 227 average time/residue: 0.1019 time to fit residues: 39.5141 Evaluate side-chains 213 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 429 SER Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 461 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 327 LEU Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 448 LEU Chi-restraints excluded: chain O residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 122 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 201 optimal weight: 30.0000 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095804 restraints weight = 32571.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092544 restraints weight = 24767.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093319 restraints weight = 21583.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093809 restraints weight = 15775.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094035 restraints weight = 14103.467| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18039 Z= 0.139 Angle : 0.681 18.945 24919 Z= 0.316 Chirality : 0.060 1.877 3207 Planarity : 0.004 0.044 3065 Dihedral : 12.196 177.116 3146 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.39 % Allowed : 20.78 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2436 helix: 2.14 (0.20), residues: 730 sheet: 0.09 (0.22), residues: 636 loop : -0.36 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 409 TYR 0.037 0.002 TYR L 267 PHE 0.023 0.001 PHE N 9 TRP 0.015 0.001 TRP O 231 HIS 0.024 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (18039) covalent geometry : angle 0.68090 / 0.32 (24919) hydrogen bonds : bond 0.03588 / 2.56 ( 897) hydrogen bonds : angle 4.33733 / 3.09 ( 2450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: K 32 LEU cc_start: 0.8613 (mt) cc_final: 0.8247 (mt) REVERT: K 42 PHE cc_start: 0.7369 (p90) cc_final: 0.7005 (p90) REVERT: J 55 TYR cc_start: 0.7524 (m-80) cc_final: 0.7078 (m-80) REVERT: I 42 PHE cc_start: 0.6613 (m-80) cc_final: 0.6101 (p90) REVERT: D 45 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7950 (mm) REVERT: L 369 MET cc_start: 0.8944 (mmm) cc_final: 0.8712 (mmt) REVERT: L 429 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8658 (t) REVERT: L 494 LYS cc_start: 0.8848 (mttt) cc_final: 0.8536 (mttp) REVERT: N 138 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8886 (mp) REVERT: N 433 GLU cc_start: 0.6872 (pt0) cc_final: 0.6550 (tt0) REVERT: N 507 MET cc_start: 0.7224 (mtp) cc_final: 0.6906 (ttm) REVERT: N 571 LYS cc_start: 0.7926 (tptt) cc_final: 0.7505 (tppt) REVERT: O 35 MET cc_start: 0.8362 (ttm) cc_final: 0.7918 (tpp) REVERT: O 62 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7328 (p0) REVERT: O 176 ASP cc_start: 0.8042 (t0) cc_final: 0.7669 (t0) outliers start: 51 outliers final: 40 residues processed: 211 average time/residue: 0.1047 time to fit residues: 37.4947 Evaluate side-chains 209 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 429 SER Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 461 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 448 LEU Chi-restraints excluded: chain O residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 200 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 138 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.140954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092917 restraints weight = 32710.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089488 restraints weight = 25805.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090432 restraints weight = 22043.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090721 restraints weight = 17032.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090974 restraints weight = 15463.876| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18039 Z= 0.181 Angle : 0.691 18.995 24919 Z= 0.328 Chirality : 0.060 1.857 3207 Planarity : 0.004 0.046 3065 Dihedral : 12.149 177.084 3146 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.32 % Allowed : 20.92 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2436 helix: 2.02 (0.20), residues: 730 sheet: 0.02 (0.22), residues: 629 loop : -0.38 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 319 TYR 0.036 0.002 TYR L 267 PHE 0.027 0.002 PHE N 9 TRP 0.015 0.001 TRP O 231 HIS 0.011 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (18039) covalent geometry : angle 0.69141 / 0.33 (24919) hydrogen bonds : bond 0.04061 / 2.90 ( 897) hydrogen bonds : angle 4.44265 / 3.16 ( 2450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: K 42 PHE cc_start: 0.7501 (p90) cc_final: 0.7142 (p90) REVERT: J 55 TYR cc_start: 0.7650 (m-80) cc_final: 0.7163 (m-80) REVERT: I 42 PHE cc_start: 0.6834 (m-80) cc_final: 0.6186 (p90) REVERT: D 45 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8038 (mm) REVERT: F 26 LEU cc_start: 0.8313 (mm) cc_final: 0.8104 (tp) REVERT: L 369 MET cc_start: 0.8966 (mmm) cc_final: 0.8742 (mmt) REVERT: L 429 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8689 (t) REVERT: L 494 LYS cc_start: 0.8902 (mttt) cc_final: 0.8577 (mttp) REVERT: N 138 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8906 (mp) REVERT: N 433 GLU cc_start: 0.7022 (pt0) cc_final: 0.6726 (pt0) REVERT: N 507 MET cc_start: 0.7278 (mtp) cc_final: 0.6852 (ttm) REVERT: N 571 LYS cc_start: 0.8038 (tptt) cc_final: 0.7621 (tppt) REVERT: O 176 ASP cc_start: 0.7977 (t0) cc_final: 0.7670 (t0) outliers start: 50 outliers final: 40 residues processed: 207 average time/residue: 0.1014 time to fit residues: 35.5579 Evaluate side-chains 206 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 429 SER Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 556 HIS Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 411 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 461 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 448 LEU Chi-restraints excluded: chain O residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 227 optimal weight: 0.0770 chunk 189 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 212 optimal weight: 0.0270 chunk 186 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.143841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096233 restraints weight = 32415.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093232 restraints weight = 25150.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094201 restraints weight = 21156.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094511 restraints weight = 16379.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094807 restraints weight = 14773.985| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18039 Z= 0.105 Angle : 0.657 19.114 24919 Z= 0.304 Chirality : 0.059 1.850 3207 Planarity : 0.004 0.045 3065 Dihedral : 11.968 178.047 3146 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.59 % Allowed : 21.51 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2436 helix: 2.17 (0.20), residues: 727 sheet: 0.17 (0.22), residues: 626 loop : -0.26 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 306 TYR 0.035 0.002 TYR L 267 PHE 0.014 0.001 PHE E 11 TRP 0.015 0.001 TRP O 231 HIS 0.008 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (18039) covalent geometry : angle 0.65700 / 0.30 (24919) hydrogen bonds : bond 0.03189 / 2.30 ( 897) hydrogen bonds : angle 4.25344 / 3.03 ( 2450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: K 42 PHE cc_start: 0.7380 (p90) cc_final: 0.6996 (p90) REVERT: J 24 ILE cc_start: 0.8674 (tp) cc_final: 0.8471 (tp) REVERT: J 55 TYR cc_start: 0.7598 (m-80) cc_final: 0.7330 (m-80) REVERT: I 42 PHE cc_start: 0.6607 (m-80) cc_final: 0.6182 (p90) REVERT: D 45 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8017 (mm) REVERT: L 369 MET cc_start: 0.8886 (mmm) cc_final: 0.8643 (mmt) REVERT: L 494 LYS cc_start: 0.8852 (mttt) cc_final: 0.8545 (mttp) REVERT: L 601 ASP cc_start: 0.7222 (p0) cc_final: 0.6782 (p0) REVERT: N 138 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8714 (mm) REVERT: N 433 GLU cc_start: 0.6893 (pt0) cc_final: 0.6550 (tt0) REVERT: N 571 LYS cc_start: 0.8025 (tptt) cc_final: 0.7555 (tppt) REVERT: O 62 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7472 (p0) REVERT: O 176 ASP cc_start: 0.7974 (t0) cc_final: 0.7704 (t0) REVERT: O 425 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8878 (p) outliers start: 39 outliers final: 32 residues processed: 205 average time/residue: 0.1017 time to fit residues: 35.5197 Evaluate side-chains 200 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 649 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 425 VAL Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 461 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 425 VAL Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 183 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 0.0070 chunk 238 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 169 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094163 restraints weight = 32537.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.090808 restraints weight = 24643.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091931 restraints weight = 21032.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092221 restraints weight = 16075.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092475 restraints weight = 14596.788| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18039 Z= 0.174 Angle : 0.679 19.030 24919 Z= 0.319 Chirality : 0.060 1.869 3207 Planarity : 0.004 0.045 3065 Dihedral : 11.961 179.266 3146 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.66 % Allowed : 21.71 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2436 helix: 2.11 (0.20), residues: 730 sheet: 0.12 (0.22), residues: 631 loop : -0.29 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 409 TYR 0.035 0.002 TYR L 267 PHE 0.026 0.002 PHE N 9 TRP 0.013 0.001 TRP O 231 HIS 0.006 0.001 HIS O 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (18039) covalent geometry : angle 0.67912 / 0.32 (24919) hydrogen bonds : bond 0.03757 / 2.68 ( 897) hydrogen bonds : angle 4.32599 / 3.07 ( 2450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.21 seconds wall clock time: 46 minutes 25.17 seconds (2785.17 seconds total)