Starting phenix.real_space_refine on Mon Apr 15 16:27:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp9_30148/04_2024/7bp9_30148_updated.pdb" } resolution = 3.6 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 24 5.49 5 S 180 5.16 5 C 22008 2.51 5 N 6246 2.21 5 O 6756 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 34": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 607": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35214 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.03, per 1000 atoms: 0.48 Number of scatterers: 35214 At special positions: 0 Unit cell: (167.99, 176.55, 100.58, 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 24 15.00 O 6756 8.00 N 6246 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=0, symmetry=0 Time building additional restraints: 14.22 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 39.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.23 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 212 through 225 removed outlier: 5.034A 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 227 through 231 removed outlier: 3.611A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' 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 319 through 334 removed outlier: 3.720A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (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 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 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 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.194A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 663 removed outlier: 4.354A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.979A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 739 No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 749 through 764 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 212 through 225 removed outlier: 5.034A 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 227 through 231 removed outlier: 3.611A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' 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 319 through 334 removed outlier: 3.720A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (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 402 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 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 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 4.193A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 663 removed outlier: 4.354A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.979A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 739 No H-bonds generated for 'chain 'B' and resid 736 through 739' Processing helix chain 'B' and resid 749 through 764 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 212 through 225 removed outlier: 5.034A 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 227 through 231 removed outlier: 3.611A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 231' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' 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 319 through 334 removed outlier: 3.720A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (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 402 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 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 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.194A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 663 removed outlier: 4.355A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 686 through 710 removed outlier: 3.980A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 739 No H-bonds generated for 'chain 'C' and resid 736 through 739' Processing helix chain 'C' and resid 749 through 764 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 212 through 225 removed outlier: 5.035A 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 227 through 231 removed outlier: 3.611A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 231' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' 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 319 through 334 removed outlier: 3.719A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (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 402 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 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 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 4.194A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 663 removed outlier: 4.354A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 686 through 710 removed outlier: 3.979A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 739 No H-bonds generated for 'chain 'D' and resid 736 through 739' Processing helix chain 'D' and resid 749 through 764 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 212 through 225 removed outlier: 5.035A 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 227 through 231 removed outlier: 3.611A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 231' Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' 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 319 through 334 removed outlier: 3.719A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (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 402 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 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 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.193A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 663 removed outlier: 4.354A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 686 through 710 removed outlier: 3.979A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 739 No H-bonds generated for 'chain 'E' and resid 736 through 739' Processing helix chain 'E' and resid 749 through 764 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 212 through 225 removed outlier: 5.034A 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 227 through 231 removed outlier: 3.612A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' 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 319 through 334 removed outlier: 3.719A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (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 402 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 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 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 4.194A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 removed outlier: 3.822A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.354A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 686 through 710 removed outlier: 3.979A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 739 No H-bonds generated for 'chain 'F' and resid 736 through 739' Processing helix chain 'F' and resid 749 through 764 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.788A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 151 through 156 removed outlier: 7.027A 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: 8.116A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 83 removed outlier: 8.787A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= H, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.027A 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: 8.115A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 83 removed outlier: 8.787A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= M, first strand: chain 'C' and resid 151 through 156 removed outlier: 7.027A 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: 8.116A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 83 removed outlier: 8.787A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= R, first strand: chain 'D' and resid 151 through 156 removed outlier: 7.027A 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: 8.115A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 83 removed outlier: 8.787A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= W, first strand: chain 'E' and resid 151 through 156 removed outlier: 7.028A 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: 8.115A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 83 removed outlier: 8.787A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AB, first strand: chain 'F' and resid 151 through 156 removed outlier: 7.027A 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: 8.115A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.732A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3186 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: 13.20 Time building geometry restraints manager: 15.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7594 1.33 - 1.45: 7136 1.45 - 1.57: 20736 1.57 - 1.69: 42 1.69 - 1.82: 288 Bond restraints: 35796 Sorted by residual: bond pdb=" CB VAL C 123 " pdb=" CG2 VAL C 123 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL B 123 " pdb=" CG2 VAL B 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.62e+00 bond pdb=" CB VAL A 123 " pdb=" CG2 VAL A 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.59e+00 bond pdb=" CB VAL D 123 " pdb=" CG2 VAL D 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.56e+00 bond pdb=" CB VAL E 123 " pdb=" CG2 VAL E 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.55e+00 ... (remaining 35791 not shown) Histogram of bond angle deviations from ideal: 98.57 - 106.08: 1178 106.08 - 113.58: 19189 113.58 - 121.08: 17546 121.08 - 128.59: 10261 128.59 - 136.09: 210 Bond angle restraints: 48384 Sorted by residual: angle pdb=" CA VAL C 38 " pdb=" CB VAL C 38 " pdb=" CG2 VAL C 38 " ideal model delta sigma weight residual 110.40 117.14 -6.74 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CA VAL F 38 " pdb=" CB VAL F 38 " pdb=" CG2 VAL F 38 " ideal model delta sigma weight residual 110.40 117.13 -6.73 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CA VAL B 38 " pdb=" CB VAL B 38 " pdb=" CG2 VAL B 38 " ideal model delta sigma weight residual 110.40 117.12 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " pdb=" CG2 VAL A 38 " ideal model delta sigma weight residual 110.40 117.12 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA VAL E 38 " pdb=" CB VAL E 38 " pdb=" CG2 VAL E 38 " ideal model delta sigma weight residual 110.40 117.10 -6.70 1.70e+00 3.46e-01 1.55e+01 ... (remaining 48379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.49: 21624 31.49 - 62.98: 516 62.98 - 94.47: 66 94.47 - 125.96: 18 125.96 - 157.45: 12 Dihedral angle restraints: 22236 sinusoidal: 9438 harmonic: 12798 Sorted by residual: dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual 300.00 142.55 157.45 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 142.59 157.41 1 2.00e+01 2.50e-03 4.62e+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 300.00 142.60 157.40 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 22233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4956 0.128 - 0.257: 432 0.257 - 0.385: 24 0.385 - 0.513: 0 0.513 - 0.642: 6 Chirality restraints: 5418 Sorted by residual: chirality pdb=" CB VAL F 38 " pdb=" CA VAL F 38 " pdb=" CG1 VAL F 38 " pdb=" CG2 VAL F 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL C 38 " pdb=" CA VAL C 38 " pdb=" CG1 VAL C 38 " pdb=" CG2 VAL C 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL B 38 " pdb=" CA VAL B 38 " pdb=" CG1 VAL B 38 " pdb=" CG2 VAL B 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 5415 not shown) Planarity restraints: 6378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 624 " -0.033 2.00e-02 2.50e+03 6.82e-02 4.65e+01 pdb=" CG ASN C 624 " 0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN C 624 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 624 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 624 " -0.033 2.00e-02 2.50e+03 6.81e-02 4.64e+01 pdb=" CG ASN A 624 " 0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN A 624 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 624 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.033 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" CG ASN B 624 " 0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " -0.039 2.00e-02 2.50e+03 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3881 2.75 - 3.29: 35676 3.29 - 3.83: 55229 3.83 - 4.36: 66953 4.36 - 4.90: 113775 Nonbonded interactions: 275514 Sorted by model distance: nonbonded pdb=" O ASP C 74 " pdb=" OD1 ASP C 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP E 74 " pdb=" OD1 ASP E 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP A 74 " pdb=" OD1 ASP A 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP D 74 " pdb=" OD1 ASP D 74 " model vdw 2.216 3.040 nonbonded pdb=" O ASP F 74 " pdb=" OD1 ASP F 74 " model vdw 2.216 3.040 ... (remaining 275509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.500 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: 0.030 Extract box with map and model: 3.730 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 94.130 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.250 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.009 0.094 35796 Z= 0.573 Angle : 1.259 10.192 48384 Z= 0.687 Chirality : 0.076 0.642 5418 Planarity : 0.008 0.068 6378 Dihedral : 14.690 157.449 13932 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 0.47 % Allowed : 5.25 % Favored : 94.28 % 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: -3.34 (0.10), residues: 4416 helix: -1.39 (0.10), residues: 1812 sheet: -2.31 (0.19), residues: 546 loop : -2.97 (0.11), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP F 551 HIS 0.011 0.002 HIS F 317 PHE 0.025 0.003 PHE D 575 TYR 0.038 0.004 TYR E 138 ARG 0.008 0.001 ARG D 65 *********************** 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 543 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 525 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 ARG cc_start: 0.7417 (mmp80) cc_final: 0.6883 (ttp-170) REVERT: A 740 MET cc_start: 0.5517 (ttp) cc_final: 0.4973 (ttp) REVERT: B 159 ARG cc_start: 0.6722 (mmt180) cc_final: 0.6334 (mmt90) REVERT: B 434 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.4330 (p0) REVERT: B 464 LEU cc_start: 0.6738 (mt) cc_final: 0.6120 (mt) REVERT: C 312 LYS cc_start: 0.6135 (mtpt) cc_final: 0.5872 (mtmt) REVERT: C 465 ARG cc_start: 0.7333 (mmp80) cc_final: 0.6734 (ttp-170) REVERT: D 159 ARG cc_start: 0.6604 (mmt180) cc_final: 0.6370 (mtt90) REVERT: D 434 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.4878 (p0) REVERT: D 464 LEU cc_start: 0.6521 (mt) cc_final: 0.6025 (mt) REVERT: D 556 GLU cc_start: 0.7977 (pm20) cc_final: 0.7733 (pm20) REVERT: E 312 LYS cc_start: 0.6458 (mtpt) cc_final: 0.6134 (mtmt) REVERT: F 159 ARG cc_start: 0.7158 (mmt180) cc_final: 0.6424 (ttm-80) REVERT: F 434 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.4805 (p0) REVERT: F 464 LEU cc_start: 0.6477 (mt) cc_final: 0.5660 (mt) REVERT: F 608 MET cc_start: 0.8589 (ttp) cc_final: 0.8322 (ttp) outliers start: 18 outliers final: 5 residues processed: 537 average time/residue: 0.6135 time to fit residues: 490.7070 Evaluate side-chains 309 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 434 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 403 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 382 GLN B 90 ASN B 226 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 90 ASN C 183 HIS C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 183 HIS E 624 ASN F 90 ASN F 226 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35796 Z= 0.236 Angle : 0.664 10.532 48384 Z= 0.313 Chirality : 0.046 0.247 5418 Planarity : 0.005 0.051 6378 Dihedral : 10.328 126.596 4981 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.03 % Allowed : 9.47 % Favored : 89.50 % 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: -2.07 (0.12), residues: 4416 helix: -0.31 (0.12), residues: 1812 sheet: -1.96 (0.19), residues: 600 loop : -2.16 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 454 HIS 0.010 0.001 HIS D 317 PHE 0.009 0.001 PHE D 563 TYR 0.026 0.002 TYR E 203 ARG 0.007 0.001 ARG A 313 *********************** 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 346 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 307 time to evaluate : 4.448 Fit side-chains REVERT: A 315 LYS cc_start: 0.5953 (tptt) cc_final: 0.5725 (tptp) REVERT: A 465 ARG cc_start: 0.7500 (mmp80) cc_final: 0.6925 (ttp-170) REVERT: B 219 MET cc_start: 0.7379 (mtp) cc_final: 0.7065 (mtp) REVERT: B 442 MET cc_start: 0.7192 (mmm) cc_final: 0.6807 (mmm) REVERT: C 183 HIS cc_start: 0.6592 (m90) cc_final: 0.6225 (m-70) REVERT: C 312 LYS cc_start: 0.6583 (mtpt) cc_final: 0.6136 (mtmt) REVERT: C 315 LYS cc_start: 0.6184 (tptt) cc_final: 0.5980 (tptp) REVERT: C 464 LEU cc_start: 0.7176 (mt) cc_final: 0.6768 (mt) REVERT: C 465 ARG cc_start: 0.7330 (mmp80) cc_final: 0.6764 (ttp-170) REVERT: D 159 ARG cc_start: 0.6794 (mmt180) cc_final: 0.6553 (mtt90) REVERT: D 442 MET cc_start: 0.6848 (mmm) cc_final: 0.6405 (mmm) REVERT: E 183 HIS cc_start: 0.6470 (m90) cc_final: 0.6033 (m-70) REVERT: E 312 LYS cc_start: 0.6609 (mtpt) cc_final: 0.6123 (mtmt) REVERT: F 159 ARG cc_start: 0.7339 (mmt180) cc_final: 0.6926 (mmm-85) REVERT: F 427 MET cc_start: 0.6728 (mmm) cc_final: 0.6466 (mmm) REVERT: F 442 MET cc_start: 0.7102 (mmt) cc_final: 0.6709 (mmm) outliers start: 39 outliers final: 25 residues processed: 327 average time/residue: 0.5542 time to fit residues: 292.6956 Evaluate side-chains 290 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 265 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 403 optimal weight: 8.9990 chunk 436 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 382 GLN A 499 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS C 499 HIS D 226 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 317 HIS ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS F 317 HIS F 382 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 35796 Z= 0.381 Angle : 0.672 9.120 48384 Z= 0.317 Chirality : 0.047 0.153 5418 Planarity : 0.005 0.057 6378 Dihedral : 9.558 134.877 4968 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.71 % Allowed : 11.50 % Favored : 86.79 % 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: -1.75 (0.12), residues: 4416 helix: -0.07 (0.12), residues: 1800 sheet: -1.58 (0.21), residues: 588 loop : -2.02 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.005 0.001 HIS B 317 PHE 0.013 0.002 PHE D 302 TYR 0.020 0.002 TYR E 203 ARG 0.013 0.001 ARG D 753 *********************** 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 341 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 276 time to evaluate : 3.919 Fit side-chains REVERT: A 315 LYS cc_start: 0.6085 (tptt) cc_final: 0.5802 (tptp) REVERT: A 740 MET cc_start: 0.5375 (ttp) cc_final: 0.5095 (mtm) REVERT: B 442 MET cc_start: 0.7184 (mmm) cc_final: 0.6762 (mmm) REVERT: C 312 LYS cc_start: 0.6673 (mtpt) cc_final: 0.6376 (mtmt) REVERT: C 315 LYS cc_start: 0.6132 (tptt) cc_final: 0.5819 (tptp) REVERT: C 442 MET cc_start: 0.7894 (mmt) cc_final: 0.7569 (mmt) REVERT: C 464 LEU cc_start: 0.7377 (mt) cc_final: 0.6949 (mt) REVERT: C 465 ARG cc_start: 0.7553 (mmp80) cc_final: 0.6851 (ttp-170) REVERT: C 740 MET cc_start: 0.5320 (ttp) cc_final: 0.5083 (ttp) REVERT: D 159 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6584 (mtt90) REVERT: D 442 MET cc_start: 0.6804 (mmm) cc_final: 0.6412 (mmt) REVERT: E 45 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6757 (tptt) REVERT: F 147 ARG cc_start: 0.6598 (tmt170) cc_final: 0.6384 (tmt170) REVERT: F 159 ARG cc_start: 0.7424 (mmt180) cc_final: 0.6843 (mmm-85) outliers start: 65 outliers final: 46 residues processed: 311 average time/residue: 0.5021 time to fit residues: 253.6512 Evaluate side-chains 309 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 263 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 0.0270 chunk 429 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 384 optimal weight: 50.0000 chunk 115 optimal weight: 40.0000 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN B 317 HIS B 735 HIS D 735 HIS E 317 HIS ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2398 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: