Starting phenix.real_space_refine on Sat Mar 23 02:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/03_2024/7bpb_30150_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 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 30 5.49 5 S 180 5.16 5 C 22008 2.51 5 N 6252 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35238 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'ADP': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.12, per 1000 atoms: 0.54 Number of scatterers: 35238 At special positions: 0 Unit cell: (169.534, 185.629, 101.935, 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 180 16.00 P 30 15.00 O 6768 8.00 N 6252 7.00 C 22008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.98 Conformation dependent library (CDL) restraints added in 6.9 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 30 sheets defined 39.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.46 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 526 through 534 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.985A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 585 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.447A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 759 " --> pdb=" O TYR A 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 444' Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 526 through 534 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 585 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 429 through 432 No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 440 through 444' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 526 through 534 Processing helix chain 'C' and resid 544 through 551 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 585 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 759 " --> pdb=" O TYR C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 335 removed outlier: 4.146A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 429 through 432 No H-bonds generated for 'chain 'D' and resid 429 through 432' Processing helix chain 'D' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 440 through 444' Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 544 through 551 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.983A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA D 585 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 686 through 713 removed outlier: 4.999A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.449A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 759 " --> pdb=" O TYR D 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 131 through 138 removed outlier: 4.682A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 429 through 432 No H-bonds generated for 'chain 'E' and resid 429 through 432' Processing helix chain 'E' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 440 through 444' Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 526 through 534 Processing helix chain 'E' and resid 544 through 551 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 579 through 585 removed outlier: 3.983A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 585 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 673 through 678 Processing helix chain 'E' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA E 759 " --> pdb=" O TYR E 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 335 removed outlier: 4.146A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 429 through 432 No H-bonds generated for 'chain 'F' and resid 429 through 432' Processing helix chain 'F' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 440 through 444' Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 526 through 534 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 585 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 673 through 678 Processing helix chain 'F' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 759 " --> pdb=" O TYR F 755 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 144 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 645 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A 517 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= G, first strand: chain 'B' and resid 144 through 147 Processing sheet with id= H, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 645 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 517 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 144 through 147 Processing sheet with id= M, first strand: chain 'C' and resid 151 through 156 removed outlier: 7.072A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 645 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 517 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= Q, first strand: chain 'D' and resid 144 through 147 Processing sheet with id= R, first strand: chain 'D' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE D 645 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR D 517 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= V, first strand: chain 'E' and resid 144 through 147 Processing sheet with id= W, first strand: chain 'E' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= AA, first strand: chain 'F' and resid 144 through 147 Processing sheet with id= AB, first strand: chain 'F' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 645 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR F 517 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1104 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.60 Time building geometry restraints manager: 16.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6660 1.32 - 1.45: 8002 1.45 - 1.57: 20828 1.57 - 1.70: 36 1.70 - 1.82: 294 Bond restraints: 35820 Sorted by residual: bond pdb=" O3A ANP E 901 " pdb=" PB ANP E 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP E 903 " pdb=" PB ANP E 903 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.57: 963 105.57 - 113.31: 19353 113.31 - 121.05: 18128 121.05 - 128.79: 9814 128.79 - 136.53: 168 Bond angle restraints: 48426 Sorted by residual: angle pdb=" PB ANP D 901 " pdb=" N3B ANP D 901 " pdb=" PG ANP D 901 " ideal model delta sigma weight residual 126.95 112.76 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" PB ANP E 901 " pdb=" N3B ANP E 901 " pdb=" PG ANP E 901 " ideal model delta sigma weight residual 126.95 112.78 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 112.79 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP E 903 " pdb=" N3B ANP E 903 " pdb=" PG ANP E 903 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP A 902 " pdb=" N3B ANP A 902 " pdb=" PG ANP A 902 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 ... (remaining 48421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 21778 34.85 - 69.71: 542 69.71 - 104.56: 36 104.56 - 139.41: 0 139.41 - 174.27: 6 Dihedral angle restraints: 22362 sinusoidal: 9564 harmonic: 12798 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.62 -91.62 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP C 902 " pdb=" O5' ADP C 902 " pdb=" PA ADP C 902 " pdb=" O2A ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.60 -91.60 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.59 -91.59 1 2.00e+01 2.50e-03 2.47e+01 ... (remaining 22359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3795 0.057 - 0.114: 1143 0.114 - 0.170: 355 0.170 - 0.227: 84 0.227 - 0.284: 41 Chirality restraints: 5418 Sorted by residual: chirality pdb=" C3' ANP A 902 " pdb=" C2' ANP A 902 " pdb=" C4' ANP A 902 " pdb=" O3' ANP A 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP E 903 " pdb=" C2' ANP E 903 " pdb=" C4' ANP E 903 " pdb=" O3' ANP E 903 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 5415 not shown) Planarity restraints: 6378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 545 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 544 " -0.062 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO D 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " -0.050 5.00e-02 4.00e+02 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 318 2.54 - 3.13: 24885 3.13 - 3.72: 55447 3.72 - 4.31: 69394 4.31 - 4.90: 110477 Nonbonded interactions: 260521 Sorted by model distance: nonbonded pdb=" CG ARG E 744 " pdb=" OE1 GLN F 763 " model vdw 1.956 3.440 nonbonded pdb=" OE1 GLN A 763 " pdb=" O ARG F 745 " model vdw 2.033 3.040 nonbonded pdb=" O ARG D 745 " pdb=" OE1 GLN E 763 " model vdw 2.038 3.040 nonbonded pdb=" CG ARG C 744 " pdb=" OE1 GLN D 763 " model vdw 2.071 3.440 nonbonded pdb=" O ARG C 745 " pdb=" OE1 GLN D 763 " model vdw 2.126 3.040 ... (remaining 260516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 766) selection = (chain 'B' and resid 20 through 766) selection = (chain 'C' and resid 20 through 766) selection = (chain 'D' and resid 20 through 766) selection = (chain 'E' and resid 20 through 766) selection = (chain 'F' and resid 20 through 766) } 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: 6.710 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: 0.000 Extract box with map and model: 12.980 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 96.470 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.151 35820 Z= 0.464 Angle : 1.118 14.194 48426 Z= 0.584 Chirality : 0.065 0.284 5418 Planarity : 0.009 0.093 6378 Dihedral : 16.099 174.269 14058 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.10), residues: 4416 helix: -3.32 (0.07), residues: 1890 sheet: -2.08 (0.17), residues: 774 loop : -2.21 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 454 HIS 0.015 0.002 HIS A 406 PHE 0.016 0.002 PHE A 152 TYR 0.014 0.002 TYR E 244 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 811 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8794 (mp) cc_final: 0.8484 (tp) REVERT: A 147 ARG cc_start: 0.6807 (ptp-110) cc_final: 0.6588 (ptp-170) REVERT: A 221 GLU cc_start: 0.8818 (pt0) cc_final: 0.8572 (pt0) REVERT: A 364 ASP cc_start: 0.8189 (p0) cc_final: 0.7914 (p0) REVERT: A 395 ASP cc_start: 0.7784 (t70) cc_final: 0.7303 (t0) REVERT: A 431 ASP cc_start: 0.8022 (t70) cc_final: 0.7691 (t0) REVERT: A 440 GLU cc_start: 0.9012 (tt0) cc_final: 0.8636 (tp30) REVERT: B 203 TYR cc_start: 0.7468 (m-10) cc_final: 0.7255 (m-10) REVERT: B 231 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8746 (ttpt) REVERT: B 244 TYR cc_start: 0.8086 (p90) cc_final: 0.7450 (p90) REVERT: B 261 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 364 ASP cc_start: 0.8226 (p0) cc_final: 0.7752 (p0) REVERT: B 388 MET cc_start: 0.8616 (tpt) cc_final: 0.8396 (tpt) REVERT: B 440 GLU cc_start: 0.9047 (tt0) cc_final: 0.8531 (tp30) REVERT: B 449 MET cc_start: 0.7647 (ppp) cc_final: 0.7059 (ppp) REVERT: B 454 TRP cc_start: 0.9040 (t60) cc_final: 0.8798 (t60) REVERT: B 543 LYS cc_start: 0.8847 (mppt) cc_final: 0.8616 (mtmt) REVERT: C 221 GLU cc_start: 0.8799 (pt0) cc_final: 0.8578 (pt0) REVERT: C 231 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9054 (mmmm) REVERT: C 364 ASP cc_start: 0.7994 (p0) cc_final: 0.7615 (p0) REVERT: C 395 ASP cc_start: 0.7824 (t70) cc_final: 0.7202 (t0) REVERT: C 431 ASP cc_start: 0.7851 (t70) cc_final: 0.7505 (t0) REVERT: C 440 GLU cc_start: 0.9102 (tt0) cc_final: 0.8672 (tp30) REVERT: C 445 LEU cc_start: 0.8602 (tp) cc_final: 0.8271 (pp) REVERT: C 449 MET cc_start: 0.7682 (ppp) cc_final: 0.7081 (ppp) REVERT: C 517 TYR cc_start: 0.8922 (p90) cc_final: 0.8412 (p90) REVERT: C 550 MET cc_start: 0.8684 (mtm) cc_final: 0.8441 (mtm) REVERT: C 709 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7996 (mmp80) REVERT: D 124 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8466 (mp0) REVERT: D 130 LEU cc_start: 0.8863 (mp) cc_final: 0.8566 (tp) REVERT: D 196 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6755 (mm-30) REVERT: D 221 GLU cc_start: 0.8789 (pt0) cc_final: 0.8395 (pm20) REVERT: D 231 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8726 (ttpt) REVERT: D 364 ASP cc_start: 0.8090 (p0) cc_final: 0.7632 (p0) REVERT: D 431 ASP cc_start: 0.7884 (t70) cc_final: 0.7473 (t0) REVERT: D 440 GLU cc_start: 0.8990 (tt0) cc_final: 0.8591 (tp30) REVERT: D 449 MET cc_start: 0.7719 (ppp) cc_final: 0.7419 (tmm) REVERT: D 508 MET cc_start: 0.7033 (tmm) cc_final: 0.6386 (tpp) REVERT: E 147 ARG cc_start: 0.6837 (ptp-110) cc_final: 0.6620 (ptp-170) REVERT: E 203 TYR cc_start: 0.7511 (m-10) cc_final: 0.7186 (m-10) REVERT: E 231 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8717 (ttpt) REVERT: E 244 TYR cc_start: 0.8098 (p90) cc_final: 0.7494 (p90) REVERT: E 261 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 364 ASP cc_start: 0.8095 (p0) cc_final: 0.7637 (p0) REVERT: E 395 ASP cc_start: 0.7829 (t70) cc_final: 0.7286 (t0) REVERT: E 440 GLU cc_start: 0.9051 (tt0) cc_final: 0.8520 (tp30) REVERT: E 449 MET cc_start: 0.7654 (ppp) cc_final: 0.7085 (ppp) REVERT: E 454 TRP cc_start: 0.9085 (t60) cc_final: 0.8711 (t60) REVERT: E 517 TYR cc_start: 0.8970 (p90) cc_final: 0.8176 (p90) REVERT: F 58 LEU cc_start: 0.9066 (tt) cc_final: 0.8772 (pp) REVERT: F 221 GLU cc_start: 0.8863 (pt0) cc_final: 0.8633 (pm20) REVERT: F 231 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8807 (ttpt) REVERT: F 302 PHE cc_start: 0.8968 (t80) cc_final: 0.8717 (t80) REVERT: F 344 MET cc_start: 0.8506 (mtp) cc_final: 0.7993 (mtp) REVERT: F 364 ASP cc_start: 0.8108 (p0) cc_final: 0.7646 (p0) REVERT: F 388 MET cc_start: 0.8763 (tpt) cc_final: 0.8506 (tpp) REVERT: F 431 ASP cc_start: 0.7549 (t70) cc_final: 0.7288 (t0) REVERT: F 440 GLU cc_start: 0.9045 (tt0) cc_final: 0.8673 (tp30) REVERT: F 449 MET cc_start: 0.7796 (ppp) cc_final: 0.7453 (tmm) REVERT: F 508 MET cc_start: 0.6695 (tmm) cc_final: 0.6243 (tpp) REVERT: F 517 TYR cc_start: 0.8940 (p90) cc_final: 0.8253 (p90) REVERT: F 550 MET cc_start: 0.8595 (mtm) cc_final: 0.8394 (mtm) outliers start: 2 outliers final: 0 residues processed: 812 average time/residue: 0.6066 time to fit residues: 737.5068 Evaluate side-chains 541 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 499 HIS C 212 GLN C 327 GLN C 458 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN F 327 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 35820 Z= 0.334 Angle : 0.729 9.266 48426 Z= 0.369 Chirality : 0.047 0.177 5418 Planarity : 0.006 0.070 6378 Dihedral : 11.398 175.863 5094 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.12), residues: 4416 helix: -1.17 (0.11), residues: 1824 sheet: -1.76 (0.17), residues: 738 loop : -1.93 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 476 HIS 0.008 0.001 HIS C 406 PHE 0.023 0.002 PHE C 363 TYR 0.021 0.002 TYR A 244 ARG 0.040 0.001 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 638 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8598 (ptt) cc_final: 0.8299 (tpp) REVERT: A 130 LEU cc_start: 0.8882 (mp) cc_final: 0.8623 (tp) REVERT: A 131 PHE cc_start: 0.8847 (t80) cc_final: 0.8562 (t80) REVERT: A 221 GLU cc_start: 0.9069 (pt0) cc_final: 0.8765 (pt0) REVERT: A 431 ASP cc_start: 0.7537 (t70) cc_final: 0.7304 (t0) REVERT: A 440 GLU cc_start: 0.9033 (tt0) cc_final: 0.8639 (tp30) REVERT: A 508 MET cc_start: 0.8620 (ptp) cc_final: 0.8130 (ptm) REVERT: A 709 ARG cc_start: 0.8304 (ttt180) cc_final: 0.7453 (ttp80) REVERT: A 740 MET cc_start: 0.5578 (ptt) cc_final: 0.5362 (ptt) REVERT: B 46 MET cc_start: 0.7805 (ptt) cc_final: 0.7596 (ptt) REVERT: B 131 PHE cc_start: 0.8885 (t80) cc_final: 0.8591 (t80) REVERT: B 163 PHE cc_start: 0.8896 (m-80) cc_final: 0.8459 (m-80) REVERT: B 368 ASP cc_start: 0.7362 (t0) cc_final: 0.7058 (p0) REVERT: B 388 MET cc_start: 0.8655 (tpt) cc_final: 0.8410 (tpt) REVERT: B 431 ASP cc_start: 0.7375 (t70) cc_final: 0.7140 (t0) REVERT: B 440 GLU cc_start: 0.9084 (tt0) cc_final: 0.8632 (tp30) REVERT: B 458 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7591 (pp30) REVERT: C 203 TYR cc_start: 0.7450 (m-10) cc_final: 0.6378 (m-10) REVERT: C 221 GLU cc_start: 0.9048 (pt0) cc_final: 0.8775 (pt0) REVERT: C 340 HIS cc_start: 0.7373 (m170) cc_final: 0.7121 (m-70) REVERT: C 426 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9146 (tptt) REVERT: C 431 ASP cc_start: 0.7647 (t70) cc_final: 0.7384 (t0) REVERT: C 440 GLU cc_start: 0.9120 (tt0) cc_final: 0.8707 (tp30) REVERT: C 458 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7654 (pp30) REVERT: C 508 MET cc_start: 0.8587 (ptp) cc_final: 0.8359 (ptm) REVERT: C 517 TYR cc_start: 0.8921 (p90) cc_final: 0.8492 (p90) REVERT: C 550 MET cc_start: 0.8695 (mtm) cc_final: 0.8421 (mtm) REVERT: D 46 MET cc_start: 0.8518 (ptt) cc_final: 0.8148 (tpp) REVERT: D 130 LEU cc_start: 0.8907 (mp) cc_final: 0.8661 (tp) REVERT: D 131 PHE cc_start: 0.8871 (t80) cc_final: 0.8589 (t80) REVERT: D 147 ARG cc_start: 0.6748 (ptp-110) cc_final: 0.6515 (ptp-170) REVERT: D 196 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6888 (mm-30) REVERT: D 221 GLU cc_start: 0.9049 (pt0) cc_final: 0.8783 (pt0) REVERT: D 244 TYR cc_start: 0.8088 (p90) cc_final: 0.7645 (p90) REVERT: D 427 MET cc_start: 0.7631 (ttt) cc_final: 0.7410 (ttt) REVERT: D 431 ASP cc_start: 0.7688 (t70) cc_final: 0.7426 (t0) REVERT: D 440 GLU cc_start: 0.8936 (tt0) cc_final: 0.8590 (tp30) REVERT: D 458 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: D 508 MET cc_start: 0.7260 (tmm) cc_final: 0.5924 (tmm) REVERT: E 131 PHE cc_start: 0.8797 (t80) cc_final: 0.8498 (t80) REVERT: E 368 ASP cc_start: 0.7415 (t0) cc_final: 0.7019 (p0) REVERT: E 388 MET cc_start: 0.8617 (tpt) cc_final: 0.8398 (tpt) REVERT: E 426 LYS cc_start: 0.9375 (tmtt) cc_final: 0.9145 (tptt) REVERT: E 431 ASP cc_start: 0.7567 (t70) cc_final: 0.7321 (t0) REVERT: E 440 GLU cc_start: 0.9107 (tt0) cc_final: 0.8637 (tp30) REVERT: E 458 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7612 (pp30) REVERT: E 712 GLU cc_start: 0.6931 (tt0) cc_final: 0.6207 (tt0) REVERT: E 744 ARG cc_start: 0.5368 (mmt-90) cc_final: 0.4878 (mmt-90) REVERT: F 131 PHE cc_start: 0.8858 (t80) cc_final: 0.8624 (t80) REVERT: F 163 PHE cc_start: 0.8833 (m-80) cc_final: 0.8468 (m-80) REVERT: F 203 TYR cc_start: 0.7667 (m-10) cc_final: 0.6825 (m-80) REVERT: F 221 GLU cc_start: 0.9032 (pt0) cc_final: 0.8786 (pt0) REVERT: F 368 ASP cc_start: 0.7670 (t0) cc_final: 0.7204 (p0) REVERT: F 388 MET cc_start: 0.8719 (tpt) cc_final: 0.8479 (tpt) REVERT: F 426 LYS cc_start: 0.9419 (tmtt) cc_final: 0.9176 (tptt) REVERT: F 431 ASP cc_start: 0.7387 (t70) cc_final: 0.7137 (t0) REVERT: F 440 GLU cc_start: 0.9108 (tt0) cc_final: 0.8698 (tp30) REVERT: F 449 MET cc_start: 0.7745 (ppp) cc_final: 0.6989 (ppp) REVERT: F 458 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7947 (pp30) REVERT: F 517 TYR cc_start: 0.8985 (p90) cc_final: 0.8445 (p90) outliers start: 5 outliers final: 0 residues processed: 643 average time/residue: 0.5559 time to fit residues: 544.4410 Evaluate side-chains 515 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 510 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 403 optimal weight: 0.0020 chunk 436 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 212 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN ** E 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35820 Z= 0.227 Angle : 0.637 10.581 48426 Z= 0.314 Chirality : 0.045 0.140 5418 Planarity : 0.005 0.066 6378 Dihedral : 11.055 179.910 5094 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4416 helix: -0.37 (0.12), residues: 1824 sheet: -1.38 (0.19), residues: 672 loop : -1.67 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 476 HIS 0.004 0.001 HIS C 406 PHE 0.022 0.001 PHE F 302 TYR 0.017 0.001 TYR B 517 ARG 0.016 0.001 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8879 (mp) cc_final: 0.8656 (tp) REVERT: A 221 GLU cc_start: 0.9069 (pt0) cc_final: 0.8741 (pt0) REVERT: A 440 GLU cc_start: 0.8878 (tt0) cc_final: 0.8574 (tp30) REVERT: A 709 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7599 (ttp80) REVERT: B 163 PHE cc_start: 0.8854 (m-80) cc_final: 0.8433 (m-80) REVERT: B 244 TYR cc_start: 0.7801 (p90) cc_final: 0.6929 (p90) REVERT: B 388 MET cc_start: 0.8634 (tpt) cc_final: 0.8410 (tpt) REVERT: B 431 ASP cc_start: 0.7272 (t70) cc_final: 0.7058 (t0) REVERT: B 440 GLU cc_start: 0.9032 (tt0) cc_final: 0.8592 (tp30) REVERT: B 449 MET cc_start: 0.7517 (ppp) cc_final: 0.6879 (ppp) REVERT: B 598 ASP cc_start: 0.8332 (p0) cc_final: 0.8035 (p0) REVERT: B 674 PHE cc_start: 0.6162 (m-10) cc_final: 0.5935 (m-10) REVERT: C 196 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6464 (mm-30) REVERT: C 221 GLU cc_start: 0.9034 (pt0) cc_final: 0.8745 (pt0) REVERT: C 244 TYR cc_start: 0.7937 (p90) cc_final: 0.6909 (p90) REVERT: C 340 HIS cc_start: 0.7272 (m170) cc_final: 0.7005 (m-70) REVERT: C 426 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9131 (tptt) REVERT: C 431 ASP cc_start: 0.7451 (t70) cc_final: 0.7245 (t0) REVERT: C 440 GLU cc_start: 0.9064 (tt0) cc_final: 0.8675 (tp30) REVERT: C 517 TYR cc_start: 0.8910 (p90) cc_final: 0.8405 (p90) REVERT: C 550 MET cc_start: 0.8671 (mtm) cc_final: 0.8408 (mtm) REVERT: C 740 MET cc_start: 0.5581 (ptt) cc_final: 0.5282 (ptt) REVERT: D 130 LEU cc_start: 0.8868 (mp) cc_final: 0.8652 (tp) REVERT: D 147 ARG cc_start: 0.6781 (ptp-110) cc_final: 0.6515 (ptp-170) REVERT: D 196 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6811 (mm-30) REVERT: D 221 GLU cc_start: 0.9020 (pt0) cc_final: 0.8732 (pt0) REVERT: D 231 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8918 (ptmt) REVERT: D 426 LYS cc_start: 0.9324 (tmtt) cc_final: 0.9064 (tptt) REVERT: D 431 ASP cc_start: 0.7574 (t70) cc_final: 0.7364 (t0) REVERT: D 440 GLU cc_start: 0.8964 (tt0) cc_final: 0.8607 (tp30) REVERT: D 449 MET cc_start: 0.7610 (ppp) cc_final: 0.7141 (ppp) REVERT: D 508 MET cc_start: 0.7324 (tmm) cc_final: 0.5907 (tmm) REVERT: D 711 ARG cc_start: 0.8748 (ttt-90) cc_final: 0.8445 (mmm-85) REVERT: E 163 PHE cc_start: 0.8814 (m-80) cc_final: 0.8395 (m-80) REVERT: E 244 TYR cc_start: 0.7865 (p90) cc_final: 0.7015 (p90) REVERT: E 426 LYS cc_start: 0.9316 (tmtt) cc_final: 0.9091 (tptt) REVERT: E 440 GLU cc_start: 0.9045 (tt0) cc_final: 0.8548 (tp30) REVERT: E 449 MET cc_start: 0.7656 (ppp) cc_final: 0.7022 (ppp) REVERT: E 712 GLU cc_start: 0.6906 (tt0) cc_final: 0.6658 (tt0) REVERT: E 744 ARG cc_start: 0.5443 (mmt-90) cc_final: 0.5024 (mmt-90) REVERT: F 163 PHE cc_start: 0.8792 (m-80) cc_final: 0.8426 (m-80) REVERT: F 221 GLU cc_start: 0.9047 (pt0) cc_final: 0.8753 (pt0) REVERT: F 244 TYR cc_start: 0.7853 (p90) cc_final: 0.7278 (p90) REVERT: F 388 MET cc_start: 0.8713 (tpt) cc_final: 0.8480 (tpt) REVERT: F 426 LYS cc_start: 0.9405 (tmtt) cc_final: 0.9139 (tptt) REVERT: F 440 GLU cc_start: 0.9063 (tt0) cc_final: 0.8676 (tp30) REVERT: F 449 MET cc_start: 0.7530 (ppp) cc_final: 0.6886 (ppp) REVERT: F 517 TYR cc_start: 0.8949 (p90) cc_final: 0.8357 (p90) REVERT: F 712 GLU cc_start: 0.7556 (tt0) cc_final: 0.7146 (mt-10) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.5215 time to fit residues: 504.8400 Evaluate side-chains 494 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 44 optimal weight: 0.0000 chunk 192 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 429 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 226 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN D 226 HIS ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 340 HIS F 36 ASN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35820 Z= 0.203 Angle : 0.612 8.494 48426 Z= 0.300 Chirality : 0.045 0.210 5418 Planarity : 0.005 0.065 6378 Dihedral : 10.848 179.761 5094 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4416 helix: -0.05 (0.12), residues: 1830 sheet: -1.14 (0.19), residues: 672 loop : -1.52 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 476 HIS 0.003 0.001 HIS C 406 PHE 0.012 0.001 PHE F 563 TYR 0.018 0.001 TYR A 244 ARG 0.008 0.001 ARG F 635 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 616 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8811 (tpp) cc_final: 0.8534 (tpt) REVERT: A 130 LEU cc_start: 0.8756 (mp) cc_final: 0.8544 (tp) REVERT: A 196 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6764 (mm-30) REVERT: A 221 GLU cc_start: 0.9070 (pt0) cc_final: 0.8750 (pt0) REVERT: A 440 GLU cc_start: 0.8789 (tt0) cc_final: 0.8560 (tp30) REVERT: A 709 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7498 (ttp80) REVERT: B 131 PHE cc_start: 0.8765 (t80) cc_final: 0.8444 (t80) REVERT: B 136 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8705 (mmmt) REVERT: B 163 PHE cc_start: 0.8894 (m-80) cc_final: 0.8463 (m-80) REVERT: B 244 TYR cc_start: 0.8058 (p90) cc_final: 0.7147 (p90) REVERT: B 388 MET cc_start: 0.8605 (tpt) cc_final: 0.8398 (tpt) REVERT: B 438 ASP cc_start: 0.7599 (p0) cc_final: 0.7246 (t70) REVERT: B 440 GLU cc_start: 0.8868 (tt0) cc_final: 0.8535 (tp30) REVERT: B 449 MET cc_start: 0.7694 (ppp) cc_final: 0.6951 (ppp) REVERT: B 508 MET cc_start: 0.7961 (ptp) cc_final: 0.7685 (ptp) REVERT: B 534 GLU cc_start: 0.8541 (pt0) cc_final: 0.8206 (pt0) REVERT: C 196 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6499 (mm-30) REVERT: C 219 MET cc_start: 0.8479 (ttm) cc_final: 0.8237 (ttm) REVERT: C 221 GLU cc_start: 0.9060 (pt0) cc_final: 0.8543 (pm20) REVERT: C 426 LYS cc_start: 0.9411 (tmtt) cc_final: 0.9134 (tptt) REVERT: C 440 GLU cc_start: 0.8984 (tt0) cc_final: 0.8613 (tp30) REVERT: C 517 TYR cc_start: 0.8904 (p90) cc_final: 0.8416 (p90) REVERT: C 550 MET cc_start: 0.8686 (mtm) cc_final: 0.8405 (mtm) REVERT: C 740 MET cc_start: 0.5569 (ptt) cc_final: 0.5325 (ptt) REVERT: D 46 MET cc_start: 0.8806 (tpp) cc_final: 0.8534 (tpt) REVERT: D 144 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7276 (mmm-85) REVERT: D 147 ARG cc_start: 0.6711 (ptp-110) cc_final: 0.6293 (ptp-170) REVERT: D 196 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6607 (mm-30) REVERT: D 221 GLU cc_start: 0.9067 (pt0) cc_final: 0.8692 (pm20) REVERT: D 231 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8917 (ptmt) REVERT: D 244 TYR cc_start: 0.7988 (p90) cc_final: 0.7749 (p90) REVERT: D 426 LYS cc_start: 0.9375 (tmtt) cc_final: 0.9107 (tptt) REVERT: D 431 ASP cc_start: 0.7385 (t70) cc_final: 0.7174 (t0) REVERT: D 440 GLU cc_start: 0.8946 (tt0) cc_final: 0.8569 (tp30) REVERT: D 449 MET cc_start: 0.7677 (ppp) cc_final: 0.7348 (ppp) REVERT: D 508 MET cc_start: 0.7304 (tmm) cc_final: 0.5730 (tmm) REVERT: E 163 PHE cc_start: 0.8889 (m-80) cc_final: 0.8455 (m-80) REVERT: E 219 MET cc_start: 0.8416 (ttm) cc_final: 0.8201 (ttm) REVERT: E 244 TYR cc_start: 0.8106 (p90) cc_final: 0.7194 (p90) REVERT: E 426 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9123 (tptt) REVERT: E 440 GLU cc_start: 0.8967 (tt0) cc_final: 0.8555 (tp30) REVERT: E 449 MET cc_start: 0.7788 (ppp) cc_final: 0.7040 (ppp) REVERT: E 599 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6770 (ttp80) REVERT: E 711 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8182 (mmm-85) REVERT: E 712 GLU cc_start: 0.6980 (tt0) cc_final: 0.6737 (tt0) REVERT: E 744 ARG cc_start: 0.5429 (mmt-90) cc_final: 0.5042 (mmt-90) REVERT: F 163 PHE cc_start: 0.8743 (m-80) cc_final: 0.8390 (m-80) REVERT: F 221 GLU cc_start: 0.9046 (pt0) cc_final: 0.8777 (pt0) REVERT: F 388 MET cc_start: 0.8643 (tpt) cc_final: 0.8394 (tpt) REVERT: F 426 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9139 (tptt) REVERT: F 440 GLU cc_start: 0.8968 (tt0) cc_final: 0.8647 (tp30) REVERT: F 449 MET cc_start: 0.7649 (ppp) cc_final: 0.6911 (ppp) REVERT: F 517 TYR cc_start: 0.8914 (p90) cc_final: 0.8401 (p90) REVERT: F 534 GLU cc_start: 0.8402 (pt0) cc_final: 0.8168 (pt0) REVERT: F 712 GLU cc_start: 0.7406 (tt0) cc_final: 0.7069 (mt-10) outliers start: 1 outliers final: 0 residues processed: 616 average time/residue: 0.5020 time to fit residues: 485.6801 Evaluate side-chains 505 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 0.1980 chunk 296 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 385 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35820 Z= 0.147 Angle : 0.589 10.119 48426 Z= 0.283 Chirality : 0.044 0.171 5418 Planarity : 0.005 0.065 6378 Dihedral : 10.387 178.919 5094 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4416 helix: 0.27 (0.13), residues: 1830 sheet: -0.87 (0.19), residues: 672 loop : -1.39 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 551 HIS 0.003 0.000 HIS C 735 PHE 0.013 0.001 PHE F 290 TYR 0.014 0.001 TYR C 244 ARG 0.007 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8705 (mp) cc_final: 0.8488 (tp) REVERT: A 136 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8606 (mmmt) REVERT: A 144 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7288 (mmm-85) REVERT: A 147 ARG cc_start: 0.6730 (ptp-110) cc_final: 0.6404 (ptp-170) REVERT: A 196 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6713 (mm-30) REVERT: A 221 GLU cc_start: 0.9032 (pt0) cc_final: 0.8715 (pt0) REVERT: A 440 GLU cc_start: 0.8727 (tt0) cc_final: 0.8461 (tp30) REVERT: A 709 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7552 (ttp80) REVERT: B 113 ARG cc_start: 0.7282 (ttt180) cc_final: 0.7080 (ttt180) REVERT: B 147 ARG cc_start: 0.6636 (ptp-110) cc_final: 0.6434 (ptp-170) REVERT: B 163 PHE cc_start: 0.8850 (m-80) cc_final: 0.8491 (m-80) REVERT: B 302 PHE cc_start: 0.9031 (t80) cc_final: 0.8813 (t80) REVERT: B 426 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9000 (tmmt) REVERT: B 438 ASP cc_start: 0.7276 (p0) cc_final: 0.6838 (t70) REVERT: B 440 GLU cc_start: 0.8797 (tt0) cc_final: 0.8477 (tp30) REVERT: B 449 MET cc_start: 0.7484 (ppp) cc_final: 0.6887 (ppp) REVERT: C 196 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6354 (mm-30) REVERT: C 219 MET cc_start: 0.8481 (ttm) cc_final: 0.8211 (ttm) REVERT: C 221 GLU cc_start: 0.9056 (pt0) cc_final: 0.8756 (pt0) REVERT: C 244 TYR cc_start: 0.7515 (p90) cc_final: 0.6758 (p90) REVERT: C 364 ASP cc_start: 0.7999 (p0) cc_final: 0.7752 (p0) REVERT: C 388 MET cc_start: 0.8602 (tpt) cc_final: 0.8355 (tpt) REVERT: C 426 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9113 (tptt) REVERT: C 440 GLU cc_start: 0.8925 (tt0) cc_final: 0.8508 (tp30) REVERT: C 517 TYR cc_start: 0.8874 (p90) cc_final: 0.8377 (p90) REVERT: C 548 LEU cc_start: 0.8275 (mt) cc_final: 0.8011 (mt) REVERT: C 550 MET cc_start: 0.8585 (mtm) cc_final: 0.8278 (mtm) REVERT: C 710 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 740 MET cc_start: 0.5443 (ptt) cc_final: 0.5168 (ptt) REVERT: D 43 GLN cc_start: 0.7882 (mm110) cc_final: 0.7619 (mm-40) REVERT: D 46 MET cc_start: 0.8808 (tpp) cc_final: 0.8220 (ptp) REVERT: D 136 LYS cc_start: 0.8800 (mmpt) cc_final: 0.8596 (mmmt) REVERT: D 144 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7245 (mmm-85) REVERT: D 147 ARG cc_start: 0.6676 (ptp-110) cc_final: 0.6221 (ptp-170) REVERT: D 196 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6611 (mm-30) REVERT: D 221 GLU cc_start: 0.9074 (pt0) cc_final: 0.8730 (pm20) REVERT: D 231 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8915 (ptmt) REVERT: D 244 TYR cc_start: 0.7822 (p90) cc_final: 0.7032 (p90) REVERT: D 426 LYS cc_start: 0.9348 (tmtt) cc_final: 0.9051 (tptt) REVERT: D 431 ASP cc_start: 0.7271 (t70) cc_final: 0.7069 (t0) REVERT: D 440 GLU cc_start: 0.8833 (tt0) cc_final: 0.8466 (tp30) REVERT: D 449 MET cc_start: 0.7439 (ppp) cc_final: 0.7193 (ppp) REVERT: D 454 TRP cc_start: 0.9075 (t60) cc_final: 0.8799 (t60) REVERT: D 508 MET cc_start: 0.7495 (tmm) cc_final: 0.7206 (ptm) REVERT: D 711 ARG cc_start: 0.8720 (ttt-90) cc_final: 0.8400 (mmm-85) REVERT: E 163 PHE cc_start: 0.8833 (m-80) cc_final: 0.8506 (m-80) REVERT: E 244 TYR cc_start: 0.7847 (p90) cc_final: 0.7124 (p90) REVERT: E 426 LYS cc_start: 0.9295 (tmtt) cc_final: 0.9086 (tptt) REVERT: E 438 ASP cc_start: 0.7430 (p0) cc_final: 0.6904 (t70) REVERT: E 440 GLU cc_start: 0.8788 (tt0) cc_final: 0.8453 (tp30) REVERT: E 449 MET cc_start: 0.7551 (ppp) cc_final: 0.6963 (ppp) REVERT: E 534 GLU cc_start: 0.8426 (pt0) cc_final: 0.8121 (pt0) REVERT: E 548 LEU cc_start: 0.8270 (mt) cc_final: 0.7958 (mt) REVERT: E 599 ARG cc_start: 0.7298 (mtp85) cc_final: 0.6877 (ttp-110) REVERT: E 712 GLU cc_start: 0.7008 (tt0) cc_final: 0.6773 (tt0) REVERT: E 744 ARG cc_start: 0.5479 (mmt-90) cc_final: 0.5065 (mmt-90) REVERT: F 163 PHE cc_start: 0.8825 (m-80) cc_final: 0.8499 (m-80) REVERT: F 221 GLU cc_start: 0.9027 (pt0) cc_final: 0.8763 (pt0) REVERT: F 244 TYR cc_start: 0.7819 (p90) cc_final: 0.7293 (p90) REVERT: F 388 MET cc_start: 0.8572 (tpt) cc_final: 0.8353 (tpt) REVERT: F 426 LYS cc_start: 0.9376 (tmtt) cc_final: 0.9108 (tptt) REVERT: F 438 ASP cc_start: 0.7476 (p0) cc_final: 0.7225 (t70) REVERT: F 440 GLU cc_start: 0.8825 (tt0) cc_final: 0.8619 (tp30) REVERT: F 449 MET cc_start: 0.7374 (ppp) cc_final: 0.6866 (ppp) REVERT: F 517 TYR cc_start: 0.8881 (p90) cc_final: 0.8311 (p90) REVERT: F 712 GLU cc_start: 0.7426 (tt0) cc_final: 0.7014 (mt-10) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.5073 time to fit residues: 532.3632 Evaluate side-chains 525 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 0.0370 chunk 386 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 429 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN E 340 HIS ** E 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 35820 Z= 0.306 Angle : 0.695 10.875 48426 Z= 0.344 Chirality : 0.047 0.204 5418 Planarity : 0.006 0.084 6378 Dihedral : 10.956 179.935 5094 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4416 helix: -0.02 (0.12), residues: 1836 sheet: -1.06 (0.20), residues: 690 loop : -1.67 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 551 HIS 0.003 0.001 HIS B 183 PHE 0.022 0.002 PHE D 563 TYR 0.020 0.002 TYR A 244 ARG 0.008 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8832 (mp) cc_final: 0.8625 (tp) REVERT: A 136 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8632 (mmmt) REVERT: A 196 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6704 (mm-30) REVERT: A 219 MET cc_start: 0.8683 (ttm) cc_final: 0.8414 (ttm) REVERT: A 221 GLU cc_start: 0.9183 (pt0) cc_final: 0.8802 (pm20) REVERT: A 231 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8853 (ptmt) REVERT: A 440 GLU cc_start: 0.8768 (tt0) cc_final: 0.8538 (tp30) REVERT: A 709 ARG cc_start: 0.8555 (ttt180) cc_final: 0.7552 (ttp80) REVERT: B 130 LEU cc_start: 0.8859 (tp) cc_final: 0.8628 (mp) REVERT: B 131 PHE cc_start: 0.8799 (t80) cc_final: 0.8575 (t80) REVERT: B 147 ARG cc_start: 0.6718 (ptp-110) cc_final: 0.6472 (ptp-170) REVERT: B 163 PHE cc_start: 0.9007 (m-80) cc_final: 0.8581 (m-80) REVERT: B 231 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8794 (ptmt) REVERT: B 438 ASP cc_start: 0.7647 (p0) cc_final: 0.7233 (t70) REVERT: B 440 GLU cc_start: 0.8871 (tt0) cc_final: 0.8513 (tp30) REVERT: B 598 ASP cc_start: 0.8439 (p0) cc_final: 0.8234 (p0) REVERT: B 710 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 147 ARG cc_start: 0.6071 (ptp-170) cc_final: 0.5862 (ptm160) REVERT: C 196 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6479 (mm-30) REVERT: C 219 MET cc_start: 0.8498 (ttm) cc_final: 0.8290 (ttm) REVERT: C 221 GLU cc_start: 0.9168 (pt0) cc_final: 0.8625 (pm20) REVERT: C 231 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8922 (ptmt) REVERT: C 364 ASP cc_start: 0.8147 (p0) cc_final: 0.7941 (p0) REVERT: C 388 MET cc_start: 0.8727 (tpt) cc_final: 0.8500 (tpt) REVERT: C 426 LYS cc_start: 0.9418 (tmtt) cc_final: 0.9013 (tmmt) REVERT: C 431 ASP cc_start: 0.7381 (t70) cc_final: 0.7128 (t0) REVERT: C 440 GLU cc_start: 0.9010 (tt0) cc_final: 0.8591 (tp30) REVERT: C 517 TYR cc_start: 0.8965 (p90) cc_final: 0.8474 (p90) REVERT: C 550 MET cc_start: 0.8661 (mtm) cc_final: 0.8417 (mtm) REVERT: C 598 ASP cc_start: 0.8212 (p0) cc_final: 0.7941 (p0) REVERT: C 740 MET cc_start: 0.5796 (ptt) cc_final: 0.5544 (ptt) REVERT: D 46 MET cc_start: 0.8915 (tpp) cc_final: 0.8703 (tpp) REVERT: D 136 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8611 (mmmt) REVERT: D 147 ARG cc_start: 0.6670 (ptp-110) cc_final: 0.6223 (ptp-170) REVERT: D 196 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6640 (mm-30) REVERT: D 219 MET cc_start: 0.8607 (ttm) cc_final: 0.8305 (ttm) REVERT: D 221 GLU cc_start: 0.9084 (pt0) cc_final: 0.8723 (pm20) REVERT: D 231 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8910 (ptmt) REVERT: D 244 TYR cc_start: 0.7873 (p90) cc_final: 0.6837 (p90) REVERT: D 426 LYS cc_start: 0.9456 (tmtt) cc_final: 0.9168 (tptt) REVERT: D 440 GLU cc_start: 0.8844 (tt0) cc_final: 0.8624 (tp30) REVERT: D 449 MET cc_start: 0.7698 (ppp) cc_final: 0.7296 (ppp) REVERT: E 130 LEU cc_start: 0.8643 (mp) cc_final: 0.8422 (tp) REVERT: E 131 PHE cc_start: 0.8754 (t80) cc_final: 0.8538 (t80) REVERT: E 163 PHE cc_start: 0.8959 (m-80) cc_final: 0.8563 (m-80) REVERT: E 426 LYS cc_start: 0.9420 (tmtt) cc_final: 0.9151 (tmmt) REVERT: E 427 MET cc_start: 0.7488 (ttt) cc_final: 0.7050 (ttt) REVERT: E 438 ASP cc_start: 0.7712 (p0) cc_final: 0.7141 (t70) REVERT: E 440 GLU cc_start: 0.8856 (tt0) cc_final: 0.8509 (tp30) REVERT: E 712 GLU cc_start: 0.6944 (tt0) cc_final: 0.6659 (tt0) REVERT: E 744 ARG cc_start: 0.5664 (mmt-90) cc_final: 0.5194 (mmt-90) REVERT: F 163 PHE cc_start: 0.8803 (m-80) cc_final: 0.8432 (m-80) REVERT: F 221 GLU cc_start: 0.9116 (pt0) cc_final: 0.8789 (pt0) REVERT: F 388 MET cc_start: 0.8575 (tpt) cc_final: 0.8362 (tpt) REVERT: F 426 LYS cc_start: 0.9471 (tmtt) cc_final: 0.9238 (tptt) REVERT: F 438 ASP cc_start: 0.7738 (p0) cc_final: 0.7464 (t70) REVERT: F 508 MET cc_start: 0.7486 (ptp) cc_final: 0.6906 (tpp) REVERT: F 517 TYR cc_start: 0.8946 (p90) cc_final: 0.8429 (p90) REVERT: F 598 ASP cc_start: 0.8164 (p0) cc_final: 0.7886 (p0) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.4839 time to fit residues: 459.5233 Evaluate side-chains 502 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 243 optimal weight: 0.5980 chunk 361 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 568 GLN B 340 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 568 GLN E 36 ASN E 340 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35820 Z= 0.184 Angle : 0.619 9.749 48426 Z= 0.301 Chirality : 0.045 0.220 5418 Planarity : 0.005 0.064 6378 Dihedral : 10.626 179.814 5094 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4416 helix: 0.36 (0.13), residues: 1812 sheet: -0.93 (0.20), residues: 678 loop : -1.50 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 476 HIS 0.007 0.001 HIS A 404 PHE 0.013 0.001 PHE A 290 TYR 0.014 0.001 TYR F 244 ARG 0.009 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8939 (tpp) cc_final: 0.8631 (tpp) REVERT: A 130 LEU cc_start: 0.8712 (mp) cc_final: 0.8501 (tp) REVERT: A 136 LYS cc_start: 0.8843 (mmpt) cc_final: 0.8639 (mmmt) REVERT: A 196 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6625 (mm-30) REVERT: A 221 GLU cc_start: 0.9143 (pt0) cc_final: 0.8747 (pm20) REVERT: A 578 GLU cc_start: 0.7238 (tt0) cc_final: 0.6990 (pt0) REVERT: A 709 ARG cc_start: 0.8522 (ttt180) cc_final: 0.7529 (ttp80) REVERT: B 131 PHE cc_start: 0.8820 (t80) cc_final: 0.8385 (t80) REVERT: B 136 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8656 (mmmt) REVERT: B 147 ARG cc_start: 0.6629 (ptp-110) cc_final: 0.6376 (ptm160) REVERT: B 162 GLU cc_start: 0.8653 (pm20) cc_final: 0.8344 (pm20) REVERT: B 163 PHE cc_start: 0.8840 (m-80) cc_final: 0.8522 (m-80) REVERT: B 231 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8784 (ptmt) REVERT: B 302 PHE cc_start: 0.9090 (t80) cc_final: 0.8826 (t80) REVERT: B 349 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8248 (mmm-85) REVERT: B 426 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9084 (tmmt) REVERT: B 427 MET cc_start: 0.7221 (ttt) cc_final: 0.6886 (ttt) REVERT: B 438 ASP cc_start: 0.7378 (p0) cc_final: 0.7008 (t70) REVERT: B 440 GLU cc_start: 0.8861 (tt0) cc_final: 0.8497 (tp30) REVERT: B 449 MET cc_start: 0.7796 (ppp) cc_final: 0.7050 (ppp) REVERT: C 196 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6345 (mm-30) REVERT: C 219 MET cc_start: 0.8456 (ttm) cc_final: 0.8189 (ttm) REVERT: C 221 GLU cc_start: 0.9145 (pt0) cc_final: 0.8717 (pm20) REVERT: C 231 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8888 (ptmt) REVERT: C 364 ASP cc_start: 0.8067 (p0) cc_final: 0.7843 (p0) REVERT: C 388 MET cc_start: 0.8687 (tpt) cc_final: 0.8450 (tpt) REVERT: C 426 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9118 (tptt) REVERT: C 440 GLU cc_start: 0.8968 (tt0) cc_final: 0.8568 (tp30) REVERT: C 517 TYR cc_start: 0.8937 (p90) cc_final: 0.8464 (p90) REVERT: C 550 MET cc_start: 0.8587 (mtm) cc_final: 0.8342 (mtm) REVERT: C 740 MET cc_start: 0.5733 (ptt) cc_final: 0.5469 (ptt) REVERT: D 46 MET cc_start: 0.8908 (tpp) cc_final: 0.8248 (ptm) REVERT: D 147 ARG cc_start: 0.6626 (ptp-110) cc_final: 0.6197 (ptp-170) REVERT: D 196 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6675 (mm-30) REVERT: D 221 GLU cc_start: 0.9081 (pt0) cc_final: 0.8728 (pm20) REVERT: D 231 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8912 (ptmt) REVERT: D 426 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9084 (tptt) REVERT: D 711 ARG cc_start: 0.8789 (ttt-90) cc_final: 0.8434 (mmm-85) REVERT: E 130 LEU cc_start: 0.8597 (mp) cc_final: 0.8341 (tp) REVERT: E 163 PHE cc_start: 0.8909 (m-80) cc_final: 0.8492 (m-80) REVERT: E 219 MET cc_start: 0.8248 (ttm) cc_final: 0.7998 (ttm) REVERT: E 438 ASP cc_start: 0.7559 (p0) cc_final: 0.6962 (t70) REVERT: E 440 GLU cc_start: 0.8793 (tt0) cc_final: 0.8467 (tp30) REVERT: E 449 MET cc_start: 0.7778 (ppp) cc_final: 0.7023 (ppp) REVERT: E 711 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8218 (mmm-85) REVERT: E 712 GLU cc_start: 0.7153 (tt0) cc_final: 0.6926 (tt0) REVERT: E 744 ARG cc_start: 0.5712 (mmt-90) cc_final: 0.5267 (mmt-90) REVERT: F 163 PHE cc_start: 0.8746 (m-80) cc_final: 0.8425 (m-80) REVERT: F 221 GLU cc_start: 0.9092 (pt0) cc_final: 0.8735 (pm20) REVERT: F 426 LYS cc_start: 0.9449 (tmtt) cc_final: 0.9169 (tptt) REVERT: F 438 ASP cc_start: 0.7389 (p0) cc_final: 0.7122 (t70) REVERT: F 517 TYR cc_start: 0.8897 (p90) cc_final: 0.8321 (p90) REVERT: F 599 ARG cc_start: 0.7260 (ttm110) cc_final: 0.7030 (ttm110) REVERT: F 712 GLU cc_start: 0.7330 (tt0) cc_final: 0.6960 (mt-10) outliers start: 0 outliers final: 0 residues processed: 605 average time/residue: 0.4916 time to fit residues: 468.3594 Evaluate side-chains 498 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35820 Z= 0.346 Angle : 0.722 9.216 48426 Z= 0.360 Chirality : 0.048 0.192 5418 Planarity : 0.006 0.064 6378 Dihedral : 11.049 179.874 5094 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4416 helix: -0.04 (0.12), residues: 1782 sheet: -1.19 (0.19), residues: 690 loop : -1.68 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 551 HIS 0.007 0.001 HIS A 404 PHE 0.026 0.002 PHE B 290 TYR 0.025 0.002 TYR B 244 ARG 0.008 0.001 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 571 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9069 (tpp) cc_final: 0.8422 (ptp) REVERT: A 136 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8666 (mmmt) REVERT: A 196 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6669 (mm-30) REVERT: A 219 MET cc_start: 0.8644 (ttm) cc_final: 0.8376 (ttm) REVERT: A 221 GLU cc_start: 0.9209 (pt0) cc_final: 0.8749 (pm20) REVERT: A 231 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8869 (ptmt) REVERT: A 449 MET cc_start: 0.7806 (tmm) cc_final: 0.7605 (tmm) REVERT: A 709 ARG cc_start: 0.8621 (ttt180) cc_final: 0.7555 (ttp80) REVERT: B 131 PHE cc_start: 0.8970 (t80) cc_final: 0.8686 (t80) REVERT: B 147 ARG cc_start: 0.6740 (ptp-110) cc_final: 0.6434 (ptm160) REVERT: B 163 PHE cc_start: 0.8815 (m-80) cc_final: 0.8412 (m-80) REVERT: B 231 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8764 (ptmt) REVERT: B 438 ASP cc_start: 0.7583 (p0) cc_final: 0.7254 (t70) REVERT: B 440 GLU cc_start: 0.8903 (tt0) cc_final: 0.8491 (tp30) REVERT: B 598 ASP cc_start: 0.8536 (p0) cc_final: 0.8294 (p0) REVERT: C 196 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6480 (mm-30) REVERT: C 219 MET cc_start: 0.8459 (ttm) cc_final: 0.8196 (ttm) REVERT: C 221 GLU cc_start: 0.9216 (pt0) cc_final: 0.8805 (pm20) REVERT: C 231 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8922 (ptmt) REVERT: C 388 MET cc_start: 0.8763 (tpt) cc_final: 0.8531 (tpt) REVERT: C 426 LYS cc_start: 0.9432 (tmtt) cc_final: 0.9034 (tmmt) REVERT: C 431 ASP cc_start: 0.7562 (t0) cc_final: 0.7278 (t0) REVERT: C 440 GLU cc_start: 0.9030 (tt0) cc_final: 0.8611 (tp30) REVERT: C 517 TYR cc_start: 0.8987 (p90) cc_final: 0.8513 (p90) REVERT: C 740 MET cc_start: 0.5865 (ptt) cc_final: 0.5561 (ptt) REVERT: D 46 MET cc_start: 0.9022 (tpp) cc_final: 0.8379 (ptp) REVERT: D 147 ARG cc_start: 0.6638 (ptp-110) cc_final: 0.6312 (ptp-170) REVERT: D 196 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6678 (mm-30) REVERT: D 219 MET cc_start: 0.8596 (ttm) cc_final: 0.8309 (ttt) REVERT: D 221 GLU cc_start: 0.9152 (pt0) cc_final: 0.8756 (pm20) REVERT: D 231 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8903 (ptmt) REVERT: D 426 LYS cc_start: 0.9436 (tmtt) cc_final: 0.9162 (tptt) REVERT: D 449 MET cc_start: 0.7578 (ppp) cc_final: 0.7366 (ppp) REVERT: E 131 PHE cc_start: 0.8831 (t80) cc_final: 0.8622 (t80) REVERT: E 163 PHE cc_start: 0.8945 (m-80) cc_final: 0.8545 (m-80) REVERT: E 231 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8745 (ptmt) REVERT: E 388 MET cc_start: 0.8210 (tpt) cc_final: 0.7933 (tpt) REVERT: E 426 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9164 (tmmt) REVERT: E 438 ASP cc_start: 0.7817 (p0) cc_final: 0.7264 (t70) REVERT: E 440 GLU cc_start: 0.8893 (tt0) cc_final: 0.8513 (tp30) REVERT: E 711 ARG cc_start: 0.8730 (ttt-90) cc_final: 0.8149 (mmm-85) REVERT: E 712 GLU cc_start: 0.7040 (tt0) cc_final: 0.6775 (tt0) REVERT: E 744 ARG cc_start: 0.5781 (mmt-90) cc_final: 0.5363 (mmt-90) REVERT: F 162 GLU cc_start: 0.8873 (pm20) cc_final: 0.8660 (pm20) REVERT: F 163 PHE cc_start: 0.8810 (m-80) cc_final: 0.8469 (m-80) REVERT: F 221 GLU cc_start: 0.9179 (pt0) cc_final: 0.8773 (pm20) REVERT: F 426 LYS cc_start: 0.9481 (tmtt) cc_final: 0.9247 (tptt) REVERT: F 438 ASP cc_start: 0.7618 (p0) cc_final: 0.7246 (t70) REVERT: F 517 TYR cc_start: 0.8956 (p90) cc_final: 0.8414 (p90) REVERT: F 598 ASP cc_start: 0.8458 (p0) cc_final: 0.8162 (p0) REVERT: F 740 MET cc_start: 0.5936 (ptt) cc_final: 0.5714 (ptt) outliers start: 3 outliers final: 0 residues processed: 571 average time/residue: 0.5041 time to fit residues: 452.6063 Evaluate side-chains 478 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 8.9990 chunk 409 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 377 optimal weight: 0.5980 chunk 397 optimal weight: 5.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 406 HIS B 36 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 406 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS F 404 HIS ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35820 Z= 0.299 Angle : 0.701 9.424 48426 Z= 0.348 Chirality : 0.047 0.174 5418 Planarity : 0.006 0.086 6378 Dihedral : 11.091 179.154 5094 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.08 % Allowed : 1.11 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 4416 helix: 0.03 (0.13), residues: 1740 sheet: -1.23 (0.19), residues: 690 loop : -1.65 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 551 HIS 0.010 0.001 HIS A 406 PHE 0.020 0.002 PHE F 290 TYR 0.016 0.002 TYR C 244 ARG 0.015 0.001 ARG B 766 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9032 (tpp) cc_final: 0.8420 (ptp) REVERT: A 136 LYS cc_start: 0.8891 (mmpt) cc_final: 0.8670 (mmmt) REVERT: A 196 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6673 (mm-30) REVERT: A 221 GLU cc_start: 0.9160 (pt0) cc_final: 0.8737 (pm20) REVERT: A 231 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8891 (ptmt) REVERT: A 709 ARG cc_start: 0.8646 (ttt180) cc_final: 0.7571 (ttp80) REVERT: B 131 PHE cc_start: 0.8966 (t80) cc_final: 0.8707 (t80) REVERT: B 147 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6347 (ptm160) REVERT: B 163 PHE cc_start: 0.8785 (m-80) cc_final: 0.8385 (m-80) REVERT: B 231 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8780 (ptmt) REVERT: B 426 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9138 (tmmt) REVERT: B 427 MET cc_start: 0.7185 (ttt) cc_final: 0.6917 (ttt) REVERT: B 438 ASP cc_start: 0.7471 (p0) cc_final: 0.7179 (t70) REVERT: B 440 GLU cc_start: 0.8872 (tt0) cc_final: 0.8515 (tp30) REVERT: B 598 ASP cc_start: 0.8508 (p0) cc_final: 0.8280 (p0) REVERT: C 219 MET cc_start: 0.8459 (ttm) cc_final: 0.8172 (ttm) REVERT: C 221 GLU cc_start: 0.9165 (pt0) cc_final: 0.8786 (pm20) REVERT: C 231 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8879 (ptmt) REVERT: C 388 MET cc_start: 0.8633 (tpt) cc_final: 0.8273 (tpt) REVERT: C 426 LYS cc_start: 0.9413 (tmtt) cc_final: 0.8955 (tmmt) REVERT: C 440 GLU cc_start: 0.9021 (tt0) cc_final: 0.8616 (tp30) REVERT: C 517 TYR cc_start: 0.8983 (p90) cc_final: 0.8495 (p90) REVERT: C 740 MET cc_start: 0.5872 (ptt) cc_final: 0.5556 (ptt) REVERT: D 46 MET cc_start: 0.9034 (tpp) cc_final: 0.8365 (ptp) REVERT: D 147 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6309 (ptp-170) REVERT: D 196 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6682 (mm-30) REVERT: D 221 GLU cc_start: 0.9124 (pt0) cc_final: 0.8697 (pm20) REVERT: D 231 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8904 (ptmt) REVERT: D 426 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9166 (tptt) REVERT: D 449 MET cc_start: 0.7576 (ppp) cc_final: 0.7365 (ppp) REVERT: D 711 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.8110 (mmm-85) REVERT: E 113 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7067 (tpt170) REVERT: E 163 PHE cc_start: 0.8811 (m-80) cc_final: 0.8452 (m-80) REVERT: E 231 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8773 (ptmt) REVERT: E 388 MET cc_start: 0.8308 (tpt) cc_final: 0.8036 (tpt) REVERT: E 426 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9135 (tmmt) REVERT: E 438 ASP cc_start: 0.7779 (p0) cc_final: 0.7244 (t70) REVERT: E 440 GLU cc_start: 0.8875 (tt0) cc_final: 0.8511 (tp30) REVERT: E 711 ARG cc_start: 0.8694 (ttt-90) cc_final: 0.8197 (mmm-85) REVERT: E 712 GLU cc_start: 0.7022 (tt0) cc_final: 0.6736 (tt0) REVERT: E 744 ARG cc_start: 0.5478 (mmt-90) cc_final: 0.5071 (mmt-90) REVERT: F 162 GLU cc_start: 0.8826 (pm20) cc_final: 0.8617 (pm20) REVERT: F 163 PHE cc_start: 0.8790 (m-80) cc_final: 0.8440 (m-80) REVERT: F 221 GLU cc_start: 0.9173 (pt0) cc_final: 0.8785 (pm20) REVERT: F 426 LYS cc_start: 0.9452 (tmtt) cc_final: 0.9203 (tptt) REVERT: F 438 ASP cc_start: 0.7618 (p0) cc_final: 0.7308 (t70) REVERT: F 517 TYR cc_start: 0.8948 (p90) cc_final: 0.8397 (p90) REVERT: F 712 GLU cc_start: 0.7189 (tt0) cc_final: 0.6791 (mt-10) outliers start: 3 outliers final: 0 residues processed: 574 average time/residue: 0.5039 time to fit residues: 454.5921 Evaluate side-chains 474 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 442 optimal weight: 1.9990 chunk 407 optimal weight: 9.9990 chunk 352 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 272 optimal weight: 0.0670 chunk 215 optimal weight: 10.0000 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 536 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 406 HIS C 536 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS E 340 HIS E 406 HIS E 536 GLN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 404 HIS F 406 HIS F 536 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35820 Z= 0.161 Angle : 0.640 9.666 48426 Z= 0.307 Chirality : 0.045 0.172 5418 Planarity : 0.005 0.068 6378 Dihedral : 10.591 179.967 5094 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.08 % Allowed : 0.13 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4416 helix: 0.44 (0.13), residues: 1770 sheet: -1.03 (0.19), residues: 678 loop : -1.50 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 551 HIS 0.016 0.002 HIS F 406 PHE 0.015 0.001 PHE C 290 TYR 0.031 0.001 TYR E 244 ARG 0.012 0.001 ARG C 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 605 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9003 (tpp) cc_final: 0.8358 (ptt) REVERT: A 196 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6625 (mm-30) REVERT: A 219 MET cc_start: 0.8629 (ttm) cc_final: 0.8338 (ttm) REVERT: A 221 GLU cc_start: 0.9102 (pt0) cc_final: 0.8688 (pm20) REVERT: A 231 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8832 (ptmt) REVERT: A 364 ASP cc_start: 0.8035 (p0) cc_final: 0.7828 (p0) REVERT: A 709 ARG cc_start: 0.8578 (ttt180) cc_final: 0.7596 (ttp80) REVERT: B 113 ARG cc_start: 0.7269 (ttt180) cc_final: 0.7025 (tpt170) REVERT: B 131 PHE cc_start: 0.8807 (t80) cc_final: 0.8470 (t80) REVERT: B 147 ARG cc_start: 0.6563 (ptp-110) cc_final: 0.6192 (ptm160) REVERT: B 162 GLU cc_start: 0.8628 (pm20) cc_final: 0.8348 (pm20) REVERT: B 163 PHE cc_start: 0.8836 (m-80) cc_final: 0.8538 (m-80) REVERT: B 196 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6952 (mm-30) REVERT: B 231 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8731 (ptmt) REVERT: B 344 MET cc_start: 0.7877 (ttm) cc_final: 0.7666 (ttm) REVERT: B 349 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8261 (mmm-85) REVERT: B 426 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9029 (tmmt) REVERT: B 427 MET cc_start: 0.7079 (ttt) cc_final: 0.6835 (ttt) REVERT: B 440 GLU cc_start: 0.8756 (tt0) cc_final: 0.8523 (tp30) REVERT: B 449 MET cc_start: 0.7815 (ppp) cc_final: 0.7073 (ppp) REVERT: B 712 GLU cc_start: 0.7212 (tt0) cc_final: 0.6941 (mt-10) REVERT: C 163 PHE cc_start: 0.8753 (m-80) cc_final: 0.8350 (m-80) REVERT: C 196 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6313 (mm-30) REVERT: C 221 GLU cc_start: 0.9101 (pt0) cc_final: 0.8702 (pm20) REVERT: C 231 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8859 (ptmt) REVERT: C 426 LYS cc_start: 0.9312 (tmtt) cc_final: 0.9060 (tptt) REVERT: C 431 ASP cc_start: 0.7477 (t70) cc_final: 0.7244 (t0) REVERT: C 440 GLU cc_start: 0.8925 (tt0) cc_final: 0.8537 (tp30) REVERT: C 517 TYR cc_start: 0.8890 (p90) cc_final: 0.8420 (p90) REVERT: C 740 MET cc_start: 0.5753 (ptt) cc_final: 0.5438 (ptt) REVERT: D 46 MET cc_start: 0.8983 (tpp) cc_final: 0.8282 (ptt) REVERT: D 147 ARG cc_start: 0.6635 (ptp-110) cc_final: 0.6337 (ptp-170) REVERT: D 196 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6619 (mm-30) REVERT: D 219 MET cc_start: 0.8545 (ttm) cc_final: 0.8235 (ttt) REVERT: D 221 GLU cc_start: 0.9024 (pt0) cc_final: 0.8610 (pm20) REVERT: D 231 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8857 (ptmt) REVERT: D 244 TYR cc_start: 0.7657 (p90) cc_final: 0.6903 (p90) REVERT: D 426 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9084 (tptt) REVERT: D 449 MET cc_start: 0.7489 (ppp) cc_final: 0.7288 (ppp) REVERT: D 454 TRP cc_start: 0.9118 (t60) cc_final: 0.8775 (t60) REVERT: E 113 ARG cc_start: 0.7267 (ttt180) cc_final: 0.6902 (tpt170) REVERT: E 162 GLU cc_start: 0.8554 (pm20) cc_final: 0.8283 (pm20) REVERT: E 163 PHE cc_start: 0.8774 (m-80) cc_final: 0.8537 (m-80) REVERT: E 196 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6933 (mm-30) REVERT: E 244 TYR cc_start: 0.7761 (p90) cc_final: 0.7254 (p90) REVERT: E 349 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8239 (mmm-85) REVERT: E 426 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8965 (tmmt) REVERT: E 438 ASP cc_start: 0.7326 (p0) cc_final: 0.6675 (t70) REVERT: E 440 GLU cc_start: 0.8778 (tt0) cc_final: 0.8468 (tp30) REVERT: E 449 MET cc_start: 0.7812 (ppp) cc_final: 0.7041 (ppp) REVERT: E 599 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7283 (ttm110) REVERT: E 711 ARG cc_start: 0.8568 (ttt-90) cc_final: 0.8128 (mmm-85) REVERT: E 712 GLU cc_start: 0.6999 (tt0) cc_final: 0.6706 (tt0) REVERT: E 744 ARG cc_start: 0.5352 (mmt-90) cc_final: 0.4798 (mmt-90) REVERT: F 163 PHE cc_start: 0.8768 (m-80) cc_final: 0.8461 (m-80) REVERT: F 219 MET cc_start: 0.8564 (ttm) cc_final: 0.8170 (ttm) REVERT: F 221 GLU cc_start: 0.9059 (pt0) cc_final: 0.8671 (pm20) REVERT: F 296 ASN cc_start: 0.9042 (t0) cc_final: 0.8529 (t0) REVERT: F 364 ASP cc_start: 0.8160 (p0) cc_final: 0.7931 (p0) REVERT: F 426 LYS cc_start: 0.9364 (tmtt) cc_final: 0.9072 (tptt) REVERT: F 438 ASP cc_start: 0.7401 (p0) cc_final: 0.6946 (t70) REVERT: F 712 GLU cc_start: 0.7263 (tt0) cc_final: 0.6899 (mt-10) outliers start: 3 outliers final: 0 residues processed: 605 average time/residue: 0.5034 time to fit residues: 478.0300 Evaluate side-chains 494 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 20.0000 chunk 375 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 352 optimal weight: 0.8980 chunk 147 optimal weight: 0.0980 chunk 362 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS F 404 HIS F 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118015 restraints weight = 79456.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121082 restraints weight = 46733.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123118 restraints weight = 31706.178| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35820 Z= 0.205 Angle : 0.639 9.329 48426 Z= 0.310 Chirality : 0.045 0.158 5418 Planarity : 0.005 0.067 6378 Dihedral : 10.674 179.938 5094 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4416 helix: 0.29 (0.13), residues: 1818 sheet: -1.03 (0.19), residues: 678 loop : -1.53 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 551 HIS 0.008 0.001 HIS A 404 PHE 0.019 0.001 PHE A 290 TYR 0.025 0.001 TYR F 244 ARG 0.010 0.001 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8540.42 seconds wall clock time: 157 minutes 13.14 seconds (9433.14 seconds total)