Starting phenix.real_space_refine on Thu Feb 22 15:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlf_24528/02_2024/7rlf_24528_updated.pdb" } resolution = 3.1 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= 0.024 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21630 2.51 5 N 6090 2.21 5 O 6618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34578 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 16.86, per 1000 atoms: 0.49 Number of scatterers: 34578 At special positions: 0 Unit cell: (169.113, 175.338, 98.5625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6618 8.00 N 6090 7.00 C 21630 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.57 Conformation dependent library (CDL) restraints added in 6.1 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 24 sheets defined 39.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.73 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.207A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 4.993A 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 233 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 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 319 through 333 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' 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 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' 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: 4.029A 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 524 through 534 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.823A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 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 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.603A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.208A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 4.992A 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 233 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 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 319 through 333 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' 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 355 through 358 Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' 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: 4.028A 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 524 through 534 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.824A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 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 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.603A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.207A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 4.993A 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 233 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 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 319 through 333 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' 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 355 through 358 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' 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: 4.029A 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 524 through 534 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.823A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 583 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 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.603A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.207A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 4.993A 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 233 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 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 319 through 333 Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' 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 355 through 358 Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' 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: 4.028A 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 524 through 534 Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.823A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 583 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 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.603A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'E' and resid 43 through 48 removed outlier: 4.207A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 4.993A 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 233 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 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 319 through 333 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' 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 355 through 358 Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' 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: 4.029A 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 524 through 534 Processing helix chain 'E' and resid 544 through 550 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.824A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 583 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 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.602A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.207A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 4.993A 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 233 Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 282 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 319 through 333 Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' 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 355 through 358 Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 424 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' 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: 4.030A 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 524 through 534 Processing helix chain 'F' and resid 544 through 550 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.823A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 583 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 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.603A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 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 151 through 156 removed outlier: 6.838A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 366 through 368 removed outlier: 7.148A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.545A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= F, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.837A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 366 through 368 removed outlier: 7.148A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.546A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= J, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.837A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 366 through 368 removed outlier: 7.147A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.546A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= N, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.838A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 366 through 368 removed outlier: 7.148A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.545A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= R, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.838A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 366 through 368 removed outlier: 7.148A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.547A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= V, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.838A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 366 through 368 removed outlier: 7.148A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.546A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 3096 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: 11.67 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11947 1.37 - 1.51: 9625 1.51 - 1.66: 13276 1.66 - 1.80: 211 1.80 - 1.95: 89 Bond restraints: 35148 Sorted by residual: bond pdb=" CD ARG A 225 " pdb=" NE ARG A 225 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.62e+00 bond pdb=" CD ARG D 113 " pdb=" NE ARG D 113 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" CD ARG E 225 " pdb=" NE ARG E 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.58e+00 bond pdb=" CD ARG C 225 " pdb=" NE ARG C 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.55e+00 bond pdb=" CD ARG F 113 " pdb=" NE ARG F 113 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.50e+00 ... (remaining 35143 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.43: 896 105.43 - 112.57: 18590 112.57 - 119.72: 11805 119.72 - 126.87: 15879 126.87 - 134.02: 380 Bond angle restraints: 47550 Sorted by residual: angle pdb=" N ASP D 121 " pdb=" CA ASP D 121 " pdb=" C ASP D 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP A 121 " pdb=" CA ASP A 121 " pdb=" C ASP A 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP E 121 " pdb=" CA ASP E 121 " pdb=" C ASP E 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ASP B 121 " pdb=" CA ASP B 121 " pdb=" C ASP B 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 angle pdb=" N ASP F 121 " pdb=" CA ASP F 121 " pdb=" C ASP F 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 ... (remaining 47545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 19289 16.22 - 32.45: 1751 32.45 - 48.67: 530 48.67 - 64.89: 198 64.89 - 81.12: 60 Dihedral angle restraints: 21828 sinusoidal: 9258 harmonic: 12570 Sorted by residual: dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " pdb=" CA PRO D 298 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 21825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2908 0.026 - 0.052: 1408 0.052 - 0.078: 556 0.078 - 0.104: 341 0.104 - 0.130: 151 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 5361 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 298 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO B 298 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 298 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.030 5.00e-02 4.00e+02 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 457 2.61 - 3.18: 30859 3.18 - 3.76: 55744 3.76 - 4.33: 76070 4.33 - 4.90: 122213 Nonbonded interactions: 285343 Sorted by model distance: nonbonded pdb=" OG1 THR A 525 " pdb="MG MG A 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR B 525 " pdb="MG MG B 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR F 525 " pdb="MG MG F 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.043 2.170 ... (remaining 285338 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.590 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 84.580 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.004 0.047 35148 Z= 0.235 Angle : 0.577 7.519 47550 Z= 0.322 Chirality : 0.043 0.130 5364 Planarity : 0.004 0.055 6234 Dihedral : 15.176 81.118 13680 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % Rotamer: Outliers : 0.19 % Allowed : 14.11 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.50 (0.14), residues: 4344 helix: 1.20 (0.13), residues: 1854 sheet: 0.28 (0.21), residues: 636 loop : -0.48 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 551 HIS 0.005 0.001 HIS E 317 PHE 0.009 0.001 PHE F 736 TYR 0.012 0.001 TYR E 138 ARG 0.005 0.000 ARG D 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 4.146 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6033 (tpt) cc_final: 0.5826 (tpt) REVERT: A 230 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8534 (t80) REVERT: A 236 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8604 (mmtm) REVERT: B 84 MET cc_start: 0.5722 (tpt) cc_final: 0.5401 (tpt) REVERT: B 344 MET cc_start: 0.8851 (mtp) cc_final: 0.8548 (ttm) REVERT: B 420 LEU cc_start: 0.8813 (mt) cc_final: 0.8570 (mt) REVERT: B 449 MET cc_start: 0.8843 (tpt) cc_final: 0.7984 (tpp) REVERT: C 84 MET cc_start: 0.5027 (tpt) cc_final: 0.4813 (tpt) REVERT: C 158 MET cc_start: 0.9254 (ttm) cc_final: 0.9030 (ttp) REVERT: D 84 MET cc_start: 0.6025 (tpt) cc_final: 0.5780 (tpt) REVERT: D 230 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8527 (t80) REVERT: E 84 MET cc_start: 0.6091 (tpt) cc_final: 0.5777 (tpt) REVERT: F 608 MET cc_start: 0.9050 (mtm) cc_final: 0.8778 (mtp) outliers start: 7 outliers final: 4 residues processed: 236 average time/residue: 0.4791 time to fit residues: 186.0081 Evaluate side-chains 174 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 35148 Z= 0.381 Angle : 0.590 8.256 47550 Z= 0.297 Chirality : 0.046 0.149 5364 Planarity : 0.005 0.060 6234 Dihedral : 9.125 59.916 4992 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.36 % Favored : 96.36 % Rotamer: Outliers : 2.69 % Allowed : 12.95 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.47 (0.14), residues: 4344 helix: 1.08 (0.13), residues: 1878 sheet: -0.05 (0.20), residues: 684 loop : -0.25 (0.17), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 551 HIS 0.005 0.001 HIS C 384 PHE 0.018 0.002 PHE D 506 TYR 0.016 0.002 TYR D 138 ARG 0.010 0.001 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 179 time to evaluate : 3.870 Fit side-chains REVERT: A 84 MET cc_start: 0.6149 (tpt) cc_final: 0.5887 (tpt) REVERT: A 230 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8616 (t80) REVERT: B 84 MET cc_start: 0.6084 (tpt) cc_final: 0.5707 (tpt) REVERT: B 161 VAL cc_start: 0.7066 (m) cc_final: 0.6741 (m) REVERT: C 158 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8865 (ttm) REVERT: D 84 MET cc_start: 0.6144 (tpt) cc_final: 0.5805 (tpt) REVERT: D 230 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8693 (t80) REVERT: E 84 MET cc_start: 0.6170 (tpt) cc_final: 0.5813 (tpt) REVERT: E 230 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: F 26 LEU cc_start: 0.8651 (mt) cc_final: 0.8392 (mt) outliers start: 100 outliers final: 28 residues processed: 269 average time/residue: 0.4167 time to fit residues: 191.8591 Evaluate side-chains 194 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 326 optimal weight: 8.9990 chunk 267 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 350 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 315 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35148 Z= 0.210 Angle : 0.509 9.060 47550 Z= 0.256 Chirality : 0.042 0.173 5364 Planarity : 0.004 0.056 6234 Dihedral : 8.810 59.615 4990 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.93 % Rotamer: Outliers : 1.45 % Allowed : 14.70 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.63 (0.14), residues: 4344 helix: 1.27 (0.13), residues: 1842 sheet: 0.02 (0.20), residues: 660 loop : -0.19 (0.17), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 551 HIS 0.002 0.001 HIS C 384 PHE 0.019 0.001 PHE A 152 TYR 0.011 0.001 TYR D 138 ARG 0.006 0.000 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 169 time to evaluate : 3.842 Fit side-chains REVERT: A 84 MET cc_start: 0.6161 (tpt) cc_final: 0.5770 (tpt) REVERT: A 230 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 449 MET cc_start: 0.8962 (tpt) cc_final: 0.8693 (tpp) REVERT: B 84 MET cc_start: 0.6018 (tpt) cc_final: 0.5617 (tpt) REVERT: D 84 MET cc_start: 0.6074 (tpt) cc_final: 0.5713 (tpt) REVERT: D 230 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8630 (t80) REVERT: E 84 MET cc_start: 0.6377 (tpt) cc_final: 0.5953 (tpt) REVERT: F 153 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (tm) outliers start: 54 outliers final: 25 residues processed: 214 average time/residue: 0.4042 time to fit residues: 151.1489 Evaluate side-chains 192 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 203 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 394 optimal weight: 0.6980 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35148 Z= 0.254 Angle : 0.515 7.565 47550 Z= 0.259 Chirality : 0.043 0.170 5364 Planarity : 0.004 0.055 6234 Dihedral : 8.611 56.319 4986 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 13.73 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.66 (0.14), residues: 4344 helix: 1.29 (0.13), residues: 1848 sheet: 0.03 (0.20), residues: 684 loop : -0.18 (0.17), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 551 HIS 0.003 0.001 HIS C 384 PHE 0.013 0.001 PHE A 152 TYR 0.009 0.001 TYR D 138 ARG 0.008 0.000 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 163 time to evaluate : 4.080 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6463 (tpt) cc_final: 0.6165 (tpt) REVERT: A 230 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 449 MET cc_start: 0.8972 (tpt) cc_final: 0.8719 (tpp) REVERT: B 60 LYS cc_start: 0.8441 (tptt) cc_final: 0.8026 (mtmm) REVERT: B 84 MET cc_start: 0.6071 (tpt) cc_final: 0.5809 (tpt) REVERT: C 146 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8274 (mp) REVERT: D 84 MET cc_start: 0.6099 (tpt) cc_final: 0.5687 (tpt) REVERT: D 230 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8703 (t80) REVERT: E 60 LYS cc_start: 0.8336 (tptt) cc_final: 0.8080 (mtmm) REVERT: F 608 MET cc_start: 0.9032 (mtm) cc_final: 0.8774 (mtm) outliers start: 95 outliers final: 44 residues processed: 249 average time/residue: 0.3915 time to fit residues: 172.9963 Evaluate side-chains 206 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 4.9990 chunk 237 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 310 optimal weight: 0.0040 chunk 172 optimal weight: 1.9990 chunk 356 optimal weight: 0.0870 chunk 288 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 overall best weight: 1.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35148 Z= 0.215 Angle : 0.505 8.110 47550 Z= 0.254 Chirality : 0.043 0.157 5364 Planarity : 0.004 0.056 6234 Dihedral : 8.424 53.857 4986 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.93 % Rotamer: Outliers : 1.80 % Allowed : 14.19 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.73 (0.14), residues: 4344 helix: 1.36 (0.13), residues: 1848 sheet: 0.09 (0.20), residues: 678 loop : -0.16 (0.17), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.004 0.001 HIS D 115 PHE 0.022 0.001 PHE E 131 TYR 0.012 0.001 TYR B 138 ARG 0.006 0.000 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 4.344 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6098 (tpt) cc_final: 0.5714 (tpt) REVERT: B 60 LYS cc_start: 0.8331 (tptt) cc_final: 0.7954 (mtmm) REVERT: B 84 MET cc_start: 0.6262 (tpt) cc_final: 0.5808 (tpt) REVERT: C 66 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: C 427 MET cc_start: 0.7613 (ppp) cc_final: 0.7124 (ppp) REVERT: D 84 MET cc_start: 0.6020 (tpt) cc_final: 0.5611 (tpt) REVERT: E 230 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8885 (m-80) outliers start: 67 outliers final: 45 residues processed: 218 average time/residue: 0.4197 time to fit residues: 159.4452 Evaluate side-chains 204 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 5.9990 chunk 376 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 chunk 103 optimal weight: 0.0070 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35148 Z= 0.240 Angle : 0.510 7.870 47550 Z= 0.257 Chirality : 0.043 0.143 5364 Planarity : 0.004 0.055 6234 Dihedral : 8.269 54.954 4982 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.71 % Favored : 96.02 % Rotamer: Outliers : 2.18 % Allowed : 14.05 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.78 (0.14), residues: 4344 helix: 1.36 (0.13), residues: 1848 sheet: 0.14 (0.20), residues: 678 loop : -0.11 (0.17), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 551 HIS 0.003 0.001 HIS A 115 PHE 0.014 0.001 PHE D 131 TYR 0.008 0.001 TYR D 138 ARG 0.008 0.000 ARG B 766 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 163 time to evaluate : 4.656 Fit side-chains REVERT: A 84 MET cc_start: 0.6035 (tpt) cc_final: 0.5663 (tpt) REVERT: B 60 LYS cc_start: 0.8569 (tptt) cc_final: 0.8009 (mtmm) REVERT: C 66 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: C 427 MET cc_start: 0.7620 (ppp) cc_final: 0.7140 (ppp) REVERT: D 84 MET cc_start: 0.6026 (tpt) cc_final: 0.5672 (tpt) REVERT: D 427 MET cc_start: 0.7424 (ppp) cc_final: 0.6731 (ppp) REVERT: E 230 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: F 66 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: F 608 MET cc_start: 0.9031 (mtm) cc_final: 0.8805 (mtm) outliers start: 81 outliers final: 47 residues processed: 235 average time/residue: 0.4251 time to fit residues: 172.0972 Evaluate side-chains 206 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 238 optimal weight: 0.0170 chunk 305 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 416 optimal weight: 0.6980 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35148 Z= 0.168 Angle : 0.491 11.577 47550 Z= 0.247 Chirality : 0.042 0.138 5364 Planarity : 0.004 0.055 6234 Dihedral : 8.043 59.763 4982 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 1.80 % Allowed : 14.35 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.86 (0.14), residues: 4344 helix: 1.44 (0.13), residues: 1848 sheet: 0.17 (0.20), residues: 678 loop : -0.07 (0.17), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 551 HIS 0.003 0.000 HIS D 115 PHE 0.022 0.001 PHE D 152 TYR 0.012 0.001 TYR E 138 ARG 0.006 0.000 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 166 time to evaluate : 3.800 Fit side-chains REVERT: A 84 MET cc_start: 0.5840 (tpt) cc_final: 0.5548 (tpt) REVERT: B 84 MET cc_start: 0.5429 (tpt) cc_final: 0.5141 (tpt) REVERT: B 449 MET cc_start: 0.8960 (tpt) cc_final: 0.8180 (tpp) REVERT: C 66 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: C 427 MET cc_start: 0.7633 (ppp) cc_final: 0.7165 (ppp) REVERT: D 84 MET cc_start: 0.6082 (tpt) cc_final: 0.5691 (tpt) REVERT: D 427 MET cc_start: 0.7425 (ppp) cc_final: 0.6739 (ppp) REVERT: E 152 PHE cc_start: 0.8067 (p90) cc_final: 0.7666 (p90) REVERT: E 230 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: E 256 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8070 (ttm-80) REVERT: F 150 ASP cc_start: 0.7441 (t0) cc_final: 0.7215 (t0) REVERT: F 449 MET cc_start: 0.8836 (tpt) cc_final: 0.8307 (tpp) outliers start: 67 outliers final: 39 residues processed: 227 average time/residue: 0.3947 time to fit residues: 156.3868 Evaluate side-chains 199 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 81 optimal weight: 0.0970 chunk 80 optimal weight: 40.0000 chunk 264 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35148 Z= 0.352 Angle : 0.567 9.230 47550 Z= 0.284 Chirality : 0.044 0.139 5364 Planarity : 0.005 0.062 6234 Dihedral : 8.265 59.551 4980 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.57 % Favored : 96.16 % Rotamer: Outliers : 1.75 % Allowed : 14.24 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.75 (0.14), residues: 4344 helix: 1.32 (0.13), residues: 1848 sheet: 0.15 (0.20), residues: 696 loop : -0.10 (0.17), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 551 HIS 0.003 0.001 HIS B 226 PHE 0.019 0.002 PHE D 152 TYR 0.008 0.001 TYR F 755 ARG 0.010 0.001 ARG E 766 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 154 time to evaluate : 5.597 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.5642 (tpt) cc_final: 0.5378 (tpt) REVERT: B 256 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (ttm-80) REVERT: C 66 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: C 159 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7180 (ptm-80) REVERT: C 427 MET cc_start: 0.7568 (ppp) cc_final: 0.7089 (ppp) REVERT: D 84 MET cc_start: 0.6461 (tpt) cc_final: 0.6244 (tpp) REVERT: E 152 PHE cc_start: 0.8085 (p90) cc_final: 0.7695 (p90) REVERT: E 230 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: E 256 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (ttm-80) REVERT: F 608 MET cc_start: 0.9042 (mtm) cc_final: 0.8834 (mtp) outliers start: 65 outliers final: 50 residues processed: 213 average time/residue: 0.4364 time to fit residues: 160.9928 Evaluate side-chains 202 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 147 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 2.9990 chunk 398 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 350 optimal weight: 0.2980 chunk 366 optimal weight: 3.9990 chunk 386 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35148 Z= 0.189 Angle : 0.508 9.779 47550 Z= 0.254 Chirality : 0.042 0.156 5364 Planarity : 0.004 0.055 6234 Dihedral : 8.000 56.945 4980 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.83 % Rotamer: Outliers : 1.48 % Allowed : 14.73 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.84 (0.14), residues: 4344 helix: 1.39 (0.13), residues: 1854 sheet: 0.16 (0.20), residues: 672 loop : -0.03 (0.17), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.002 0.000 HIS D 115 PHE 0.020 0.001 PHE D 152 TYR 0.011 0.001 TYR E 138 ARG 0.006 0.000 ARG B 766 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.5641 (tpt) cc_final: 0.5421 (tpt) REVERT: C 66 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: C 427 MET cc_start: 0.7620 (ppp) cc_final: 0.7154 (ppp) REVERT: E 152 PHE cc_start: 0.8084 (p90) cc_final: 0.7691 (p90) REVERT: E 230 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: E 256 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (ttm-80) outliers start: 55 outliers final: 45 residues processed: 200 average time/residue: 0.4003 time to fit residues: 140.2283 Evaluate side-chains 198 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 5.9990 chunk 410 optimal weight: 3.9990 chunk 250 optimal weight: 0.0870 chunk 194 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 396 optimal weight: 0.0980 chunk 342 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 264 optimal weight: 0.2980 chunk 210 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35148 Z= 0.169 Angle : 0.494 10.484 47550 Z= 0.245 Chirality : 0.042 0.147 5364 Planarity : 0.004 0.056 6234 Dihedral : 7.656 59.515 4980 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.20 % Rotamer: Outliers : 1.40 % Allowed : 14.94 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.93 (0.14), residues: 4344 helix: 1.48 (0.13), residues: 1848 sheet: 0.22 (0.20), residues: 666 loop : -0.00 (0.17), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.002 0.000 HIS D 115 PHE 0.019 0.001 PHE D 152 TYR 0.006 0.001 TYR D 138 ARG 0.005 0.000 ARG E 766 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 3.976 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.5430 (tpt) cc_final: 0.5145 (tpt) REVERT: A 442 MET cc_start: 0.9106 (tpt) cc_final: 0.8884 (tpp) REVERT: B 84 MET cc_start: 0.5600 (tpt) cc_final: 0.5400 (tpt) REVERT: B 219 MET cc_start: 0.8442 (mtm) cc_final: 0.8124 (ptp) REVERT: B 449 MET cc_start: 0.8997 (tpt) cc_final: 0.8230 (tpp) REVERT: C 66 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: D 84 MET cc_start: 0.6574 (tpp) cc_final: 0.6368 (tpt) REVERT: E 219 MET cc_start: 0.8460 (mtm) cc_final: 0.8091 (ptp) REVERT: E 449 MET cc_start: 0.8963 (tpt) cc_final: 0.8217 (tpp) REVERT: F 608 MET cc_start: 0.9032 (mtm) cc_final: 0.8804 (mtm) outliers start: 52 outliers final: 44 residues processed: 207 average time/residue: 0.4065 time to fit residues: 147.6176 Evaluate side-chains 194 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.068745 restraints weight = 69377.443| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.17 r_work: 0.2661 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35148 Z= 0.310 Angle : 0.541 8.524 47550 Z= 0.270 Chirality : 0.044 0.158 5364 Planarity : 0.004 0.057 6234 Dihedral : 7.833 60.849 4980 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.50 % Favored : 96.36 % Rotamer: Outliers : 1.40 % Allowed : 15.19 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.86 (0.14), residues: 4344 helix: 1.40 (0.13), residues: 1848 sheet: 0.22 (0.21), residues: 660 loop : -0.03 (0.17), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 551 HIS 0.002 0.001 HIS E 226 PHE 0.035 0.002 PHE D 363 TYR 0.011 0.001 TYR C 138 ARG 0.009 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.52 seconds wall clock time: 109 minutes 43.73 seconds (6583.73 seconds total)