Starting phenix.real_space_refine on Fri Feb 23 17:30:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcq_8399/02_2024/5tcq_8399_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 24720 2.51 5 N 6855 2.21 5 O 7515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39180 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "C" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "D" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "E" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "F" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "G" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "H" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "I" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "J" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "K" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "L" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "M" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "N" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "O" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2612 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Time building chain proxies: 20.32, per 1000 atoms: 0.52 Number of scatterers: 39180 At special positions: 0 Unit cell: (159.03, 159.03, 126.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 7515 8.00 N 6855 7.00 C 24720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.75 Conformation dependent library (CDL) restraints added in 8.0 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9360 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 34 sheets defined 21.7% alpha, 66.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 284 through 298 Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 486 through 490 Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 525 through 537 Processing helix chain 'C' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 284 through 298 Processing helix chain 'D' and resid 343 through 348 Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 486 through 490 Processing helix chain 'D' and resid 493 through 497 Processing helix chain 'D' and resid 525 through 537 Processing helix chain 'D' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 554 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 284 through 298 Processing helix chain 'E' and resid 343 through 348 Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 486 through 490 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 525 through 537 Processing helix chain 'E' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR E 553 " --> pdb=" O TRP E 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 554 " --> pdb=" O VAL E 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 284 through 298 Processing helix chain 'F' and resid 343 through 348 Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 486 through 490 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 525 through 537 Processing helix chain 'F' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR F 553 " --> pdb=" O TRP F 549 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 284 through 298 Processing helix chain 'G' and resid 343 through 348 Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'G' and resid 486 through 490 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 525 through 537 Processing helix chain 'G' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR G 553 " --> pdb=" O TRP G 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 554 " --> pdb=" O VAL G 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 284 through 298 Processing helix chain 'H' and resid 343 through 348 Processing helix chain 'H' and resid 440 through 444 Processing helix chain 'H' and resid 486 through 490 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 525 through 537 Processing helix chain 'H' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR H 553 " --> pdb=" O TRP H 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 554 " --> pdb=" O VAL H 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 273 through 275 No H-bonds generated for 'chain 'I' and resid 273 through 275' Processing helix chain 'I' and resid 284 through 298 Processing helix chain 'I' and resid 343 through 348 Processing helix chain 'I' and resid 440 through 444 Processing helix chain 'I' and resid 486 through 490 Processing helix chain 'I' and resid 493 through 497 Processing helix chain 'I' and resid 525 through 537 Processing helix chain 'I' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR I 553 " --> pdb=" O TRP I 549 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU I 554 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 273 through 275 No H-bonds generated for 'chain 'J' and resid 273 through 275' Processing helix chain 'J' and resid 284 through 298 Processing helix chain 'J' and resid 343 through 348 Processing helix chain 'J' and resid 440 through 444 Processing helix chain 'J' and resid 486 through 490 Processing helix chain 'J' and resid 493 through 497 Processing helix chain 'J' and resid 525 through 537 Processing helix chain 'J' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR J 553 " --> pdb=" O TRP J 549 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU J 554 " --> pdb=" O VAL J 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 273 through 275 No H-bonds generated for 'chain 'K' and resid 273 through 275' Processing helix chain 'K' and resid 284 through 298 Processing helix chain 'K' and resid 343 through 348 Processing helix chain 'K' and resid 440 through 444 Processing helix chain 'K' and resid 486 through 490 Processing helix chain 'K' and resid 493 through 497 Processing helix chain 'K' and resid 525 through 537 Processing helix chain 'K' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR K 553 " --> pdb=" O TRP K 549 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU K 554 " --> pdb=" O VAL K 550 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 284 through 298 Processing helix chain 'L' and resid 343 through 348 Processing helix chain 'L' and resid 440 through 444 Processing helix chain 'L' and resid 486 through 490 Processing helix chain 'L' and resid 493 through 497 Processing helix chain 'L' and resid 525 through 537 Processing helix chain 'L' and resid 547 through 556 removed outlier: 5.373A pdb=" N TYR L 553 " --> pdb=" O TRP L 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU L 554 " --> pdb=" O VAL L 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 216 Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'M' and resid 284 through 298 Processing helix chain 'M' and resid 343 through 348 Processing helix chain 'M' and resid 440 through 444 Processing helix chain 'M' and resid 486 through 490 Processing helix chain 'M' and resid 493 through 497 Processing helix chain 'M' and resid 525 through 537 Processing helix chain 'M' and resid 547 through 556 removed outlier: 5.371A pdb=" N TYR M 553 " --> pdb=" O TRP M 549 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU M 554 " --> pdb=" O VAL M 550 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 216 Processing helix chain 'N' and resid 273 through 275 No H-bonds generated for 'chain 'N' and resid 273 through 275' Processing helix chain 'N' and resid 284 through 298 Processing helix chain 'N' and resid 343 through 348 Processing helix chain 'N' and resid 440 through 444 Processing helix chain 'N' and resid 486 through 490 Processing helix chain 'N' and resid 493 through 497 Processing helix chain 'N' and resid 525 through 537 Processing helix chain 'N' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR N 553 " --> pdb=" O TRP N 549 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU N 554 " --> pdb=" O VAL N 550 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 216 Processing helix chain 'O' and resid 273 through 275 No H-bonds generated for 'chain 'O' and resid 273 through 275' Processing helix chain 'O' and resid 284 through 298 Processing helix chain 'O' and resid 343 through 348 Processing helix chain 'O' and resid 440 through 444 Processing helix chain 'O' and resid 486 through 490 Processing helix chain 'O' and resid 493 through 497 Processing helix chain 'O' and resid 525 through 537 Processing helix chain 'O' and resid 547 through 556 removed outlier: 5.372A pdb=" N TYR O 553 " --> pdb=" O TRP O 549 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU O 554 " --> pdb=" O VAL O 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 339 removed outlier: 6.578A pdb=" N GLY A 336 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 356 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 338 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA B 358 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 336 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 356 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B 338 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA C 358 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 336 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 356 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 338 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA D 358 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 303 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 513 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU D 468 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU D 467 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN E 376 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL D 469 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY E 336 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL F 356 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER E 338 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA F 358 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS F 303 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 513 " --> pdb=" O LEU F 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU F 468 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU F 467 " --> pdb=" O GLN G 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN G 376 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL F 469 " --> pdb=" O LEU G 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS G 303 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE G 513 " --> pdb=" O LEU G 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU G 468 " --> pdb=" O ILE G 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU G 467 " --> pdb=" O GLN H 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN H 376 " --> pdb=" O LEU G 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 469 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS H 303 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 513 " --> pdb=" O LEU H 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU H 468 " --> pdb=" O ILE H 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU H 467 " --> pdb=" O GLN I 376 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N GLN I 376 " --> pdb=" O LEU H 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL H 469 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS I 303 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 513 " --> pdb=" O LEU I 468 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU I 468 " --> pdb=" O ILE I 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU I 467 " --> pdb=" O GLN J 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN J 376 " --> pdb=" O LEU I 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL I 469 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS J 303 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE J 513 " --> pdb=" O LEU J 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU J 468 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU J 467 " --> pdb=" O GLN K 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN K 376 " --> pdb=" O LEU J 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL J 469 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS K 303 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE K 513 " --> pdb=" O LEU K 468 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU K 468 " --> pdb=" O ILE K 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU K 467 " --> pdb=" O GLN L 376 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N GLN L 376 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL K 469 " --> pdb=" O LEU L 374 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY L 336 " --> pdb=" O ALA M 354 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL M 356 " --> pdb=" O GLY L 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER L 338 " --> pdb=" O VAL M 356 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA M 358 " --> pdb=" O SER L 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY M 336 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL N 356 " --> pdb=" O GLY M 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER M 338 " --> pdb=" O VAL N 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA N 358 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY N 336 " --> pdb=" O ALA O 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL O 356 " --> pdb=" O GLY N 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER N 338 " --> pdb=" O VAL O 356 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA O 358 " --> pdb=" O SER N 338 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS O 303 " --> pdb=" O ILE O 518 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE O 513 " --> pdb=" O LEU O 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU O 468 " --> pdb=" O ILE O 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU O 467 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN A 376 " --> pdb=" O LEU O 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL O 469 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 483 removed outlier: 16.070A pdb=" N LEU A 467 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN B 376 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 469 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS B 303 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 513 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU B 468 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU B 467 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN C 376 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 469 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS C 303 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 513 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU C 468 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 16.068A pdb=" N LEU C 467 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN D 376 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 469 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 336 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL E 356 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER D 338 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA E 358 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS E 303 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 513 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU E 468 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU E 467 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N GLN F 376 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL E 469 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY F 336 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL G 356 " --> pdb=" O GLY F 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER F 338 " --> pdb=" O VAL G 356 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA G 358 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY G 336 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL H 356 " --> pdb=" O GLY G 336 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER G 338 " --> pdb=" O VAL H 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA H 358 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY H 336 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL I 356 " --> pdb=" O GLY H 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER H 338 " --> pdb=" O VAL I 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA I 358 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY I 336 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL J 356 " --> pdb=" O GLY I 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER I 338 " --> pdb=" O VAL J 356 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA J 358 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY J 336 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL K 356 " --> pdb=" O GLY J 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER J 338 " --> pdb=" O VAL K 356 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA K 358 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY K 336 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL L 356 " --> pdb=" O GLY K 336 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER K 338 " --> pdb=" O VAL L 356 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA L 358 " --> pdb=" O SER K 338 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS L 303 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE L 513 " --> pdb=" O LEU L 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU L 468 " --> pdb=" O ILE L 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU L 467 " --> pdb=" O GLN M 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN M 376 " --> pdb=" O LEU L 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL L 469 " --> pdb=" O LEU M 374 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS M 303 " --> pdb=" O ILE M 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE M 513 " --> pdb=" O LEU M 468 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU M 468 " --> pdb=" O ILE M 513 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LEU M 467 " --> pdb=" O GLN N 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN N 376 " --> pdb=" O LEU M 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL M 469 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS N 303 " --> pdb=" O ILE N 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE N 513 " --> pdb=" O LEU N 468 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU N 468 " --> pdb=" O ILE N 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU N 467 " --> pdb=" O GLN O 376 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N GLN O 376 " --> pdb=" O LEU N 467 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL N 469 " --> pdb=" O LEU O 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS A 303 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.900A pdb=" N HIS A 303 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 513 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU A 468 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N LEU A 467 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLN B 376 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 469 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 392 removed outlier: 12.887A pdb=" N THR A 405 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP A 433 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 407 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR B 405 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ASP B 433 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 407 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR C 405 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP C 433 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY C 407 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR D 405 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ASP D 433 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D 407 " --> pdb=" O GLY D 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR E 405 " --> pdb=" O ASP E 433 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ASP E 433 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY E 407 " --> pdb=" O GLY E 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR F 405 " --> pdb=" O ASP F 433 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ASP F 433 " --> pdb=" O THR F 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY F 407 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR G 405 " --> pdb=" O ASP G 433 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ASP G 433 " --> pdb=" O THR G 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY G 407 " --> pdb=" O GLY G 431 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR H 405 " --> pdb=" O ASP H 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP H 433 " --> pdb=" O THR H 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY H 407 " --> pdb=" O GLY H 431 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR I 405 " --> pdb=" O ASP I 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP I 433 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY I 407 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR J 405 " --> pdb=" O ASP J 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP J 433 " --> pdb=" O THR J 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY J 407 " --> pdb=" O GLY J 431 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR K 405 " --> pdb=" O ASP K 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP K 433 " --> pdb=" O THR K 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY K 407 " --> pdb=" O GLY K 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR L 405 " --> pdb=" O ASP L 433 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ASP L 433 " --> pdb=" O THR L 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY L 407 " --> pdb=" O GLY L 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR M 405 " --> pdb=" O ASP M 433 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP M 433 " --> pdb=" O THR M 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY M 407 " --> pdb=" O GLY M 431 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR N 405 " --> pdb=" O ASP N 433 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ASP N 433 " --> pdb=" O THR N 405 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY N 407 " --> pdb=" O GLY N 431 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N THR O 405 " --> pdb=" O ASP O 433 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ASP O 433 " --> pdb=" O THR O 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY O 407 " --> pdb=" O GLY O 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AA8, first strand: chain 'B' and resid 193 through 197 Processing sheet with id=AA9, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'C' and resid 193 through 197 Processing sheet with id=AB2, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AB3, first strand: chain 'D' and resid 193 through 197 Processing sheet with id=AB4, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB5, first strand: chain 'E' and resid 193 through 197 Processing sheet with id=AB6, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AB7, first strand: chain 'F' and resid 193 through 197 Processing sheet with id=AB8, first strand: chain 'G' and resid 174 through 175 Processing sheet with id=AB9, first strand: chain 'G' and resid 193 through 197 Processing sheet with id=AC1, first strand: chain 'H' and resid 174 through 175 Processing sheet with id=AC2, first strand: chain 'H' and resid 193 through 197 Processing sheet with id=AC3, first strand: chain 'I' and resid 174 through 175 Processing sheet with id=AC4, first strand: chain 'I' and resid 193 through 197 Processing sheet with id=AC5, first strand: chain 'J' and resid 174 through 175 Processing sheet with id=AC6, first strand: chain 'J' and resid 193 through 197 Processing sheet with id=AC7, first strand: chain 'K' and resid 174 through 175 Processing sheet with id=AC8, first strand: chain 'K' and resid 193 through 197 Processing sheet with id=AC9, first strand: chain 'L' and resid 174 through 175 Processing sheet with id=AD1, first strand: chain 'L' and resid 193 through 197 Processing sheet with id=AD2, first strand: chain 'M' and resid 174 through 175 Processing sheet with id=AD3, first strand: chain 'M' and resid 193 through 197 Processing sheet with id=AD4, first strand: chain 'N' and resid 174 through 175 Processing sheet with id=AD5, first strand: chain 'N' and resid 193 through 197 Processing sheet with id=AD6, first strand: chain 'O' and resid 174 through 175 Processing sheet with id=AD7, first strand: chain 'O' and resid 193 through 197 3038 hydrogen bonds defined for protein. 8394 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: 16.03 Time building geometry restraints manager: 15.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8249 1.32 - 1.44: 8137 1.44 - 1.56: 23199 1.56 - 1.68: 0 1.68 - 1.80: 180 Bond restraints: 39765 Sorted by residual: bond pdb=" CA ARG G 397 " pdb=" C ARG G 397 " ideal model delta sigma weight residual 1.526 1.496 0.030 9.20e-03 1.18e+04 1.06e+01 bond pdb=" CA ARG B 397 " pdb=" C ARG B 397 " ideal model delta sigma weight residual 1.526 1.496 0.030 9.20e-03 1.18e+04 1.05e+01 bond pdb=" CA ARG M 397 " pdb=" C ARG M 397 " ideal model delta sigma weight residual 1.526 1.497 0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" CA ARG F 397 " pdb=" C ARG F 397 " ideal model delta sigma weight residual 1.526 1.497 0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" CA ARG A 397 " pdb=" C ARG A 397 " ideal model delta sigma weight residual 1.526 1.497 0.029 9.20e-03 1.18e+04 1.02e+01 ... (remaining 39760 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.48: 676 104.48 - 111.78: 18845 111.78 - 119.09: 14465 119.09 - 126.39: 19414 126.39 - 133.70: 480 Bond angle restraints: 53880 Sorted by residual: angle pdb=" C TYR L 272 " pdb=" N PRO L 273 " pdb=" CA PRO L 273 " ideal model delta sigma weight residual 119.32 130.13 -10.81 1.14e+00 7.69e-01 8.99e+01 angle pdb=" C TYR I 272 " pdb=" N PRO I 273 " pdb=" CA PRO I 273 " ideal model delta sigma weight residual 119.32 130.10 -10.78 1.14e+00 7.69e-01 8.93e+01 angle pdb=" C TYR H 272 " pdb=" N PRO H 273 " pdb=" CA PRO H 273 " ideal model delta sigma weight residual 119.32 130.09 -10.77 1.14e+00 7.69e-01 8.93e+01 angle pdb=" C TYR E 272 " pdb=" N PRO E 273 " pdb=" CA PRO E 273 " ideal model delta sigma weight residual 119.32 130.08 -10.76 1.14e+00 7.69e-01 8.91e+01 angle pdb=" C TYR G 272 " pdb=" N PRO G 273 " pdb=" CA PRO G 273 " ideal model delta sigma weight residual 119.32 130.08 -10.76 1.14e+00 7.69e-01 8.90e+01 ... (remaining 53875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 23625 14.98 - 29.95: 480 29.95 - 44.93: 90 44.93 - 59.90: 45 59.90 - 74.88: 45 Dihedral angle restraints: 24285 sinusoidal: 9810 harmonic: 14475 Sorted by residual: dihedral pdb=" CA ASP B 544 " pdb=" CB ASP B 544 " pdb=" CG ASP B 544 " pdb=" OD1 ASP B 544 " ideal model delta sinusoidal sigma weight residual -30.00 -86.14 56.14 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP K 544 " pdb=" CB ASP K 544 " pdb=" CG ASP K 544 " pdb=" OD1 ASP K 544 " ideal model delta sinusoidal sigma weight residual -30.00 -86.12 56.12 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP L 544 " pdb=" CB ASP L 544 " pdb=" CG ASP L 544 " pdb=" OD1 ASP L 544 " ideal model delta sinusoidal sigma weight residual -30.00 -86.12 56.12 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 24282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3227 0.043 - 0.086: 2041 0.086 - 0.129: 897 0.129 - 0.172: 225 0.172 - 0.215: 30 Chirality restraints: 6420 Sorted by residual: chirality pdb=" CA ASN I 340 " pdb=" N ASN I 340 " pdb=" C ASN I 340 " pdb=" CB ASN I 340 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN D 340 " pdb=" N ASN D 340 " pdb=" C ASN D 340 " pdb=" CB ASN D 340 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN N 340 " pdb=" N ASN N 340 " pdb=" C ASN N 340 " pdb=" CB ASN N 340 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6417 not shown) Planarity restraints: 6885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 514 " 0.106 5.00e-02 4.00e+02 1.63e-01 4.25e+01 pdb=" N PRO G 515 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO G 515 " 0.092 5.00e-02 4.00e+02 pdb=" CD PRO G 515 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 514 " -0.107 5.00e-02 4.00e+02 1.63e-01 4.25e+01 pdb=" N PRO L 515 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO L 515 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO L 515 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 514 " -0.107 5.00e-02 4.00e+02 1.63e-01 4.24e+01 pdb=" N PRO M 515 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO M 515 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO M 515 " -0.083 5.00e-02 4.00e+02 ... (remaining 6882 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 18156 2.94 - 3.43: 33007 3.43 - 3.92: 63743 3.92 - 4.41: 69713 4.41 - 4.90: 122005 Nonbonded interactions: 306624 Sorted by model distance: nonbonded pdb=" OG SER I 328 " pdb=" O VAL I 337 " model vdw 2.447 2.440 nonbonded pdb=" OG SER E 328 " pdb=" O VAL E 337 " model vdw 2.448 2.440 nonbonded pdb=" OG SER H 328 " pdb=" O VAL H 337 " model vdw 2.448 2.440 nonbonded pdb=" OG SER G 328 " pdb=" O VAL G 337 " model vdw 2.448 2.440 nonbonded pdb=" OG SER C 328 " pdb=" O VAL C 337 " model vdw 2.448 2.440 ... (remaining 306619 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.930 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 103.720 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.013 0.052 39765 Z= 0.831 Angle : 1.542 13.132 53880 Z= 1.024 Chirality : 0.063 0.215 6420 Planarity : 0.012 0.163 6885 Dihedral : 8.283 74.876 14925 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 2.71 % Allowed : 3.31 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.03 (0.12), residues: 4980 helix: -1.65 (0.16), residues: 870 sheet: 0.92 (0.09), residues: 2655 loop : -0.58 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.006 TRP C 309 HIS 0.006 0.002 HIS C 303 PHE 0.030 0.006 PHE F 289 TYR 0.025 0.005 TYR J 553 ARG 0.006 0.001 ARG O 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 4.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 VAL cc_start: 0.8259 (t) cc_final: 0.8015 (m) REVERT: F 306 LEU cc_start: 0.7943 (tp) cc_final: 0.7737 (tp) REVERT: J 306 LEU cc_start: 0.7939 (tp) cc_final: 0.7737 (tp) REVERT: J 447 LEU cc_start: 0.7484 (mt) cc_final: 0.7114 (tp) REVERT: K 183 MET cc_start: 0.7046 (mtt) cc_final: 0.6833 (mtt) REVERT: N 306 LEU cc_start: 0.7742 (tp) cc_final: 0.7161 (tt) REVERT: N 382 ILE cc_start: 0.9037 (mp) cc_final: 0.8640 (mm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.5447 time to fit residues: 270.2058 Evaluate side-chains 128 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 417 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 449 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39765 Z= 0.249 Angle : 0.642 7.129 53880 Z= 0.355 Chirality : 0.046 0.171 6420 Planarity : 0.006 0.081 6885 Dihedral : 4.639 16.946 5415 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.61 % Allowed : 2.06 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.12), residues: 4980 helix: 0.10 (0.18), residues: 780 sheet: 1.16 (0.09), residues: 2715 loop : -0.49 (0.19), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 309 HIS 0.002 0.001 HIS D 303 PHE 0.018 0.002 PHE I 486 TYR 0.018 0.002 TYR N 499 ARG 0.008 0.000 ARG I 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5372 (mmt90) cc_final: 0.5031 (mtt-85) REVERT: H 513 ILE cc_start: 0.9160 (mm) cc_final: 0.8832 (tp) REVERT: L 363 LYS cc_start: 0.8200 (tttt) cc_final: 0.7920 (ttpp) REVERT: N 382 ILE cc_start: 0.8777 (mp) cc_final: 0.8300 (mm) REVERT: O 409 MET cc_start: 0.7890 (ttp) cc_final: 0.7296 (ttp) outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 0.5394 time to fit residues: 177.7439 Evaluate side-chains 139 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 382 ILE Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 389 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 374 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 450 optimal weight: 8.9990 chunk 486 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 446 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN D 506 ASN F 506 ASN G 506 ASN I 506 ASN J 506 ASN M 506 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 39765 Z= 0.337 Angle : 0.640 8.117 53880 Z= 0.346 Chirality : 0.046 0.168 6420 Planarity : 0.005 0.068 6885 Dihedral : 4.734 20.183 5415 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 0.77 % Allowed : 3.40 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.69 (0.12), residues: 4980 helix: 0.30 (0.19), residues: 780 sheet: 1.16 (0.09), residues: 2685 loop : -0.69 (0.18), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 309 HIS 0.003 0.001 HIS A 403 PHE 0.022 0.002 PHE M 289 TYR 0.018 0.002 TYR C 195 ARG 0.004 0.000 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 5.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5981 (mmt90) cc_final: 0.5514 (mmt90) REVERT: J 512 MET cc_start: 0.7392 (mtm) cc_final: 0.7163 (mtp) REVERT: N 382 ILE cc_start: 0.8743 (mp) cc_final: 0.8351 (mp) REVERT: O 409 MET cc_start: 0.8081 (ttp) cc_final: 0.7529 (ttp) outliers start: 34 outliers final: 14 residues processed: 162 average time/residue: 0.4862 time to fit residues: 137.0983 Evaluate side-chains 132 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 389 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 451 optimal weight: 0.2980 chunk 478 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 428 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39765 Z= 0.223 Angle : 0.566 12.202 53880 Z= 0.302 Chirality : 0.045 0.212 6420 Planarity : 0.005 0.064 6885 Dihedral : 4.566 18.281 5415 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.53 % Rotamer: Outliers : 0.79 % Allowed : 4.38 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.79 (0.12), residues: 4980 helix: 0.67 (0.20), residues: 780 sheet: 1.21 (0.10), residues: 2685 loop : -0.78 (0.18), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 309 HIS 0.002 0.000 HIS A 403 PHE 0.019 0.002 PHE N 289 TYR 0.014 0.001 TYR K 472 ARG 0.003 0.000 ARG H 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 4.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5934 (mmt90) cc_final: 0.5667 (mmt90) REVERT: F 384 ASP cc_start: 0.8493 (t0) cc_final: 0.8233 (t0) REVERT: N 382 ILE cc_start: 0.8721 (mp) cc_final: 0.8263 (mp) REVERT: O 409 MET cc_start: 0.8071 (ttp) cc_final: 0.7863 (tmm) outliers start: 35 outliers final: 17 residues processed: 161 average time/residue: 0.4777 time to fit residues: 134.9385 Evaluate side-chains 139 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 197 optimal weight: 0.0170 chunk 408 optimal weight: 20.0000 chunk 330 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 429 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN F 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 39765 Z= 0.339 Angle : 0.634 12.572 53880 Z= 0.332 Chirality : 0.046 0.206 6420 Planarity : 0.005 0.065 6885 Dihedral : 4.742 18.414 5415 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 1.47 % Allowed : 3.85 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.68 (0.12), residues: 4980 helix: 0.48 (0.20), residues: 780 sheet: 1.24 (0.10), residues: 2700 loop : -1.01 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 309 HIS 0.003 0.001 HIS G 403 PHE 0.024 0.002 PHE M 289 TYR 0.017 0.002 TYR C 195 ARG 0.004 0.000 ARG G 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 131 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5793 (mmt90) cc_final: 0.5468 (mmm-85) REVERT: M 409 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7054 (ttp) REVERT: N 382 ILE cc_start: 0.8731 (mp) cc_final: 0.8373 (mp) REVERT: O 397 ARG cc_start: 0.4398 (mtp85) cc_final: 0.4135 (mtp85) REVERT: O 409 MET cc_start: 0.8073 (ttp) cc_final: 0.7540 (ttp) outliers start: 65 outliers final: 46 residues processed: 182 average time/residue: 0.4875 time to fit residues: 153.9887 Evaluate side-chains 167 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 120 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 378 ASN Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 389 PHE Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 2.9990 chunk 430 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 478 optimal weight: 4.9990 chunk 397 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN E 506 ASN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39765 Z= 0.273 Angle : 0.593 11.764 53880 Z= 0.310 Chirality : 0.045 0.228 6420 Planarity : 0.005 0.063 6885 Dihedral : 4.638 20.439 5415 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.59 % Allowed : 4.06 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.12), residues: 4980 helix: 0.66 (0.20), residues: 780 sheet: 1.26 (0.10), residues: 2730 loop : -1.05 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 309 HIS 0.002 0.001 HIS E 303 PHE 0.019 0.002 PHE M 289 TYR 0.013 0.002 TYR C 195 ARG 0.007 0.000 ARG I 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 126 time to evaluate : 5.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 378 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: M 409 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7018 (ttp) REVERT: N 382 ILE cc_start: 0.8680 (mp) cc_final: 0.8376 (mp) REVERT: O 409 MET cc_start: 0.8070 (ttp) cc_final: 0.7528 (ttp) outliers start: 70 outliers final: 52 residues processed: 184 average time/residue: 0.4871 time to fit residues: 155.7310 Evaluate side-chains 174 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 120 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 389 PHE Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 349 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 403 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 477 optimal weight: 0.0870 chunk 298 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN E 216 GLN I 421 GLN K 421 GLN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 39765 Z= 0.335 Angle : 0.635 12.489 53880 Z= 0.329 Chirality : 0.046 0.216 6420 Planarity : 0.005 0.065 6885 Dihedral : 4.777 21.798 5415 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 1.81 % Allowed : 4.15 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.12), residues: 4980 helix: 0.54 (0.19), residues: 780 sheet: 1.21 (0.10), residues: 2730 loop : -1.09 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 309 HIS 0.002 0.001 HIS E 303 PHE 0.023 0.002 PHE M 289 TYR 0.016 0.002 TYR C 195 ARG 0.004 0.000 ARG G 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 128 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.6266 (mmt90) cc_final: 0.6028 (mmt90) REVERT: I 202 MET cc_start: 0.6601 (mmm) cc_final: 0.6213 (mmm) REVERT: M 378 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8272 (m-40) REVERT: M 409 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7056 (ttp) REVERT: N 382 ILE cc_start: 0.8670 (mp) cc_final: 0.8455 (mp) REVERT: O 409 MET cc_start: 0.8065 (ttp) cc_final: 0.7534 (ttp) outliers start: 80 outliers final: 65 residues processed: 195 average time/residue: 0.4546 time to fit residues: 154.5583 Evaluate side-chains 186 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 119 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 ASN Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 424 MET Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 284 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 375 optimal weight: 30.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39765 Z= 0.198 Angle : 0.566 14.392 53880 Z= 0.292 Chirality : 0.045 0.189 6420 Planarity : 0.004 0.062 6885 Dihedral : 4.542 24.175 5415 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 1.61 % Allowed : 4.67 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.12), residues: 4980 helix: 0.92 (0.20), residues: 780 sheet: 1.25 (0.10), residues: 2760 loop : -1.01 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.002 0.000 HIS E 303 PHE 0.017 0.002 PHE N 289 TYR 0.012 0.001 TYR N 499 ARG 0.004 0.000 ARG O 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 135 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.6121 (mmt90) cc_final: 0.5401 (mmt90) REVERT: I 202 MET cc_start: 0.6475 (mmm) cc_final: 0.6258 (mmm) REVERT: J 382 ILE cc_start: 0.8889 (mt) cc_final: 0.8652 (mt) REVERT: M 378 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8280 (m-40) REVERT: M 409 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (ttp) REVERT: N 382 ILE cc_start: 0.8626 (mp) cc_final: 0.8237 (mt) outliers start: 71 outliers final: 58 residues processed: 194 average time/residue: 0.4926 time to fit residues: 165.0126 Evaluate side-chains 183 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 123 time to evaluate : 5.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 ASN Chi-restraints excluded: chain E residue 389 PHE Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 419 ASP Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 424 MET Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 3.9990 chunk 457 optimal weight: 0.9980 chunk 417 optimal weight: 5.9990 chunk 444 optimal weight: 0.9990 chunk 456 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 420 optimal weight: 0.0770 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 39765 Z= 0.251 Angle : 0.584 13.629 53880 Z= 0.301 Chirality : 0.045 0.198 6420 Planarity : 0.005 0.064 6885 Dihedral : 4.557 21.123 5415 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 4.76 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.12), residues: 4980 helix: 0.93 (0.20), residues: 780 sheet: 1.22 (0.10), residues: 2745 loop : -0.93 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 309 HIS 0.002 0.001 HIS E 303 PHE 0.018 0.002 PHE M 289 TYR 0.013 0.001 TYR C 195 ARG 0.004 0.000 ARG L 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 129 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.6130 (mmt90) cc_final: 0.5660 (mmt90) REVERT: J 382 ILE cc_start: 0.8899 (mt) cc_final: 0.8666 (mt) REVERT: M 378 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: M 409 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7013 (ttp) outliers start: 72 outliers final: 66 residues processed: 188 average time/residue: 0.4608 time to fit residues: 150.2258 Evaluate side-chains 192 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 124 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 ASN Chi-restraints excluded: chain E residue 389 PHE Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain I residue 510 VAL Chi-restraints excluded: chain I residue 512 MET Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 419 ASP Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 424 MET Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 443 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 493 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 392 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 303 optimal weight: 3.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39765 Z= 0.212 Angle : 0.572 13.509 53880 Z= 0.293 Chirality : 0.045 0.191 6420 Planarity : 0.005 0.062 6885 Dihedral : 4.488 21.591 5415 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 1.66 % Allowed : 4.90 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.90 (0.12), residues: 4980 helix: 1.08 (0.20), residues: 780 sheet: 1.23 (0.10), residues: 2745 loop : -0.90 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 309 HIS 0.002 0.000 HIS O 303 PHE 0.017 0.002 PHE N 289 TYR 0.012 0.001 TYR N 499 ARG 0.016 0.000 ARG N 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 127 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 MET cc_start: 0.7075 (mmm) cc_final: 0.6865 (mmm) REVERT: J 382 ILE cc_start: 0.8886 (mt) cc_final: 0.8649 (mt) REVERT: M 378 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: M 409 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6954 (ttp) outliers start: 73 outliers final: 65 residues processed: 187 average time/residue: 0.4784 time to fit residues: 155.7255 Evaluate side-chains 189 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 122 time to evaluate : 4.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 ASN Chi-restraints excluded: chain E residue 389 PHE Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 419 ASP Chi-restraints excluded: chain I residue 512 MET Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 419 ASP Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 424 MET Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 362 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 393 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067324 restraints weight = 76173.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070262 restraints weight = 39722.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072124 restraints weight = 26864.039| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39765 Z= 0.199 Angle : 0.555 12.216 53880 Z= 0.286 Chirality : 0.045 0.188 6420 Planarity : 0.005 0.062 6885 Dihedral : 4.436 22.212 5415 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 1.59 % Allowed : 4.85 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 4980 helix: 1.20 (0.20), residues: 780 sheet: 1.25 (0.10), residues: 2745 loop : -0.87 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.002 0.000 HIS E 303 PHE 0.017 0.001 PHE L 289 TYR 0.012 0.001 TYR N 499 ARG 0.011 0.000 ARG N 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5342.02 seconds wall clock time: 101 minutes 0.86 seconds (6060.86 seconds total)