Starting phenix.real_space_refine on Thu Nov 20 21:28:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_8399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_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 { model { file = "/net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_8399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_8399_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_8399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tcq_8399/11_2025/5tcq_8399.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39180 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 3.89, per 1000 atoms: 0.10 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 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: 1.63 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: 10.83 Time building geometry restraints manager: 4.16 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: 0.00 - 2.63: 49585 2.63 - 5.25: 3672 5.25 - 7.88: 501 7.88 - 10.51: 92 10.51 - 13.13: 30 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 3.040 nonbonded pdb=" OG SER E 328 " pdb=" O VAL E 337 " model vdw 2.448 3.040 nonbonded pdb=" OG SER H 328 " pdb=" O VAL H 337 " model vdw 2.448 3.040 nonbonded pdb=" OG SER G 328 " pdb=" O VAL G 337 " model vdw 2.448 3.040 nonbonded pdb=" OG SER C 328 " pdb=" O VAL C 337 " model vdw 2.448 3.040 ... (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 Time spend for trying shortcut: 0.15 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: 2.430 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.120 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- 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= 0.769 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (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 ARG 0.006 0.001 ARG O 551 TYR 0.025 0.005 TYR J 553 PHE 0.030 0.006 PHE F 289 TRP 0.026 0.006 TRP C 309 HIS 0.006 0.002 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.01266 (39765) covalent geometry : angle 1.54239 (53880) hydrogen bonds : bond 0.15197 ( 2659) hydrogen bonds : angle 7.19360 ( 8394) *********************** 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 to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 306 LEU cc_start: 0.7943 (tp) cc_final: 0.7743 (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: 0.7115 (tp) REVERT: K 183 MET cc_start: 0.7046 (mtt) cc_final: 0.6830 (mtt) REVERT: N 306 LEU cc_start: 0.7742 (tp) cc_final: 0.7163 (tt) REVERT: N 382 ILE cc_start: 0.9037 (mp) cc_final: 0.8644 (mm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2444 time to fit residues: 122.0622 Evaluate side-chains 130 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.101336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076037 restraints weight = 74355.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078935 restraints weight = 44897.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079803 restraints weight = 30522.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080596 restraints weight = 26806.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080646 restraints weight = 24839.545| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2333 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= 0.160 Angle : 0.624 6.782 53880 Z= 0.347 Chirality : 0.046 0.171 6420 Planarity : 0.006 0.068 6885 Dihedral : 4.637 17.147 5415 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.46 % Allowed : 2.31 % Favored : 97.23 % Rotamer: Outliers : 0.48 % Allowed : 2.13 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 4980 helix: 0.14 (0.18), residues: 780 sheet: 1.12 (0.09), residues: 2685 loop : -0.50 (0.19), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 397 TYR 0.018 0.002 TYR N 499 PHE 0.019 0.002 PHE I 486 TRP 0.010 0.001 TRP F 325 HIS 0.002 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00339 (39765) covalent geometry : angle 0.62357 (53880) hydrogen bonds : bond 0.04829 ( 2659) hydrogen bonds : angle 5.15140 ( 8394) *********************** 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 202 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7372 (tt) REVERT: B 292 MET cc_start: 0.8438 (mmp) cc_final: 0.8232 (mmm) REVERT: D 393 LEU cc_start: 0.7529 (mt) cc_final: 0.7287 (tp) REVERT: G 447 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7111 (tp) REVERT: H 513 ILE cc_start: 0.9429 (mm) cc_final: 0.9108 (tp) REVERT: J 183 MET cc_start: 0.8338 (mtm) cc_final: 0.7987 (mpp) REVERT: J 363 LYS cc_start: 0.8491 (tttt) cc_final: 0.8141 (ttpp) REVERT: J 389 PHE cc_start: 0.7451 (m-80) cc_final: 0.7217 (m-10) REVERT: J 447 LEU cc_start: 0.7904 (mt) cc_final: 0.7669 (tt) REVERT: K 306 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8613 (tt) REVERT: K 397 ARG cc_start: 0.4327 (mmt180) cc_final: 0.3956 (mtt-85) REVERT: L 363 LYS cc_start: 0.8608 (tttt) cc_final: 0.8198 (ttpp) REVERT: L 496 LEU cc_start: 0.9304 (mt) cc_final: 0.8960 (tt) REVERT: L 513 ILE cc_start: 0.9347 (mm) cc_final: 0.9115 (mm) REVERT: M 363 LYS cc_start: 0.8649 (tttt) cc_final: 0.8294 (ttpp) REVERT: N 382 ILE cc_start: 0.8770 (mp) cc_final: 0.8373 (mm) outliers start: 21 outliers final: 6 residues processed: 195 average time/residue: 0.2289 time to fit residues: 75.3173 Evaluate side-chains 138 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain L residue 382 ILE 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 191 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 216 GLN G 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069278 restraints weight = 75063.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071987 restraints weight = 44598.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073173 restraints weight = 30134.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073346 restraints weight = 27141.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073432 restraints weight = 25864.326| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 39765 Z= 0.296 Angle : 0.733 8.693 53880 Z= 0.389 Chirality : 0.048 0.184 6420 Planarity : 0.005 0.069 6885 Dihedral : 4.986 24.473 5415 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 0.75 % Allowed : 3.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.12), residues: 4980 helix: -0.05 (0.19), residues: 780 sheet: 1.07 (0.09), residues: 2685 loop : -0.84 (0.18), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 370 TYR 0.026 0.003 TYR K 553 PHE 0.027 0.003 PHE M 511 TRP 0.028 0.002 TRP L 309 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00705 (39765) covalent geometry : angle 0.73283 (53880) hydrogen bonds : bond 0.05561 ( 2659) hydrogen bonds : angle 5.03772 ( 8394) *********************** 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 180 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.6043 (mmt90) cc_final: 0.5687 (mmt90) REVERT: F 496 LEU cc_start: 0.9374 (mt) cc_final: 0.9102 (tt) REVERT: J 183 MET cc_start: 0.8555 (mtm) cc_final: 0.8058 (mpp) REVERT: J 447 LEU cc_start: 0.8294 (mt) cc_final: 0.7932 (tp) REVERT: J 512 MET cc_start: 0.7879 (mtm) cc_final: 0.7571 (mtp) REVERT: K 397 ARG cc_start: 0.6046 (mmt180) cc_final: 0.5628 (mtt-85) REVERT: L 202 MET cc_start: 0.7772 (mtt) cc_final: 0.7549 (mtt) REVERT: L 496 LEU cc_start: 0.9392 (mt) cc_final: 0.9098 (tt) REVERT: M 363 LYS cc_start: 0.8508 (tttt) cc_final: 0.8283 (ttpp) REVERT: M 424 MET cc_start: 0.8745 (mtm) cc_final: 0.8402 (mpp) REVERT: M 496 LEU cc_start: 0.9423 (mt) cc_final: 0.9176 (tt) REVERT: N 382 ILE cc_start: 0.8764 (mp) cc_final: 0.8465 (mp) REVERT: O 409 MET cc_start: 0.8785 (ttp) cc_final: 0.8161 (ttp) outliers start: 33 outliers final: 16 residues processed: 168 average time/residue: 0.2304 time to fit residues: 65.9739 Evaluate side-chains 138 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 513 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain L residue 424 MET 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 236 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 489 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 488 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 368 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.069583 restraints weight = 74994.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.072578 restraints weight = 39431.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074512 restraints weight = 27025.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075675 restraints weight = 21586.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076379 restraints weight = 18892.841| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39765 Z= 0.135 Angle : 0.565 13.101 53880 Z= 0.300 Chirality : 0.045 0.189 6420 Planarity : 0.004 0.062 6885 Dihedral : 4.612 19.560 5415 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 0.61 % Allowed : 4.08 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4980 helix: 0.62 (0.19), residues: 780 sheet: 1.13 (0.10), residues: 2715 loop : -0.87 (0.18), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 397 TYR 0.015 0.001 TYR N 499 PHE 0.018 0.002 PHE C 389 TRP 0.011 0.001 TRP E 540 HIS 0.001 0.000 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00298 (39765) covalent geometry : angle 0.56469 (53880) hydrogen bonds : bond 0.04279 ( 2659) hydrogen bonds : angle 4.64010 ( 8394) *********************** 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 173 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5864 (mmt90) cc_final: 0.5526 (mtt-85) REVERT: E 496 LEU cc_start: 0.9431 (mp) cc_final: 0.9147 (tt) REVERT: F 496 LEU cc_start: 0.9402 (mt) cc_final: 0.9128 (tt) REVERT: J 183 MET cc_start: 0.8706 (mtm) cc_final: 0.8004 (mpp) REVERT: J 447 LEU cc_start: 0.8090 (mt) cc_final: 0.7687 (tt) REVERT: J 512 MET cc_start: 0.7947 (mtm) cc_final: 0.7729 (mtp) REVERT: K 496 LEU cc_start: 0.9296 (mp) cc_final: 0.8796 (tt) REVERT: L 202 MET cc_start: 0.7800 (mtt) cc_final: 0.7543 (mtt) REVERT: L 363 LYS cc_start: 0.8727 (tttt) cc_final: 0.8301 (ttmm) REVERT: L 409 MET cc_start: 0.8787 (ttp) cc_final: 0.8546 (tmm) REVERT: L 496 LEU cc_start: 0.9448 (mt) cc_final: 0.9044 (tt) REVERT: L 513 ILE cc_start: 0.9259 (mm) cc_final: 0.8918 (tp) REVERT: M 363 LYS cc_start: 0.8612 (tttt) cc_final: 0.8355 (ttpp) REVERT: M 496 LEU cc_start: 0.9496 (mt) cc_final: 0.9162 (tt) REVERT: N 382 ILE cc_start: 0.8586 (mp) cc_final: 0.8275 (mp) REVERT: O 397 ARG cc_start: 0.6428 (mtp85) cc_final: 0.5931 (mtp85) outliers start: 27 outliers final: 13 residues processed: 164 average time/residue: 0.2212 time to fit residues: 62.1769 Evaluate side-chains 146 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 389 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 72 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 442 optimal weight: 0.8980 chunk 351 optimal weight: 10.0000 chunk 468 optimal weight: 2.9990 chunk 454 optimal weight: 6.9990 chunk 391 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.072626 restraints weight = 74591.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075601 restraints weight = 44285.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076970 restraints weight = 28873.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077137 restraints weight = 25972.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077041 restraints weight = 24134.455| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39765 Z= 0.137 Angle : 0.546 10.436 53880 Z= 0.290 Chirality : 0.045 0.181 6420 Planarity : 0.005 0.062 6885 Dihedral : 4.492 18.351 5415 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.79 % Allowed : 4.06 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4980 helix: 0.88 (0.20), residues: 780 sheet: 1.19 (0.10), residues: 2685 loop : -0.90 (0.18), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 397 TYR 0.013 0.001 TYR N 499 PHE 0.018 0.002 PHE N 289 TRP 0.011 0.001 TRP L 309 HIS 0.002 0.000 HIS J 288 Details of bonding type rmsd covalent geometry : bond 0.00309 (39765) covalent geometry : angle 0.54571 (53880) hydrogen bonds : bond 0.04175 ( 2659) hydrogen bonds : angle 4.48729 ( 8394) *********************** 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 177 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 397 ARG cc_start: 0.5938 (mmt90) cc_final: 0.5641 (mtt-85) REVERT: F 496 LEU cc_start: 0.9285 (mt) cc_final: 0.8947 (tt) REVERT: H 183 MET cc_start: 0.7733 (mtp) cc_final: 0.7393 (mtt) REVERT: H 363 LYS cc_start: 0.8425 (tttt) cc_final: 0.8218 (ttpp) REVERT: J 183 MET cc_start: 0.8499 (mtm) cc_final: 0.7977 (mpp) REVERT: J 447 LEU cc_start: 0.8132 (mt) cc_final: 0.7781 (tt) REVERT: K 496 LEU cc_start: 0.9209 (mp) cc_final: 0.8837 (tt) REVERT: L 363 LYS cc_start: 0.8628 (tttt) cc_final: 0.8390 (ttmm) REVERT: L 496 LEU cc_start: 0.9359 (mt) cc_final: 0.9087 (tt) REVERT: L 513 ILE cc_start: 0.9197 (mm) cc_final: 0.8994 (tp) REVERT: M 496 LEU cc_start: 0.9383 (mt) cc_final: 0.9175 (tt) REVERT: N 382 ILE cc_start: 0.8805 (mp) cc_final: 0.8486 (mp) REVERT: O 397 ARG cc_start: 0.6578 (mtp85) cc_final: 0.6028 (mtp85) REVERT: O 409 MET cc_start: 0.8644 (ttp) cc_final: 0.8425 (tmm) outliers start: 35 outliers final: 18 residues processed: 169 average time/residue: 0.2317 time to fit residues: 67.3031 Evaluate side-chains 151 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 513 ILE 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 D residue 294 VAL Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR 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 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 164 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 492 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 413 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 F 421 GLN F 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.070526 restraints weight = 75914.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073331 restraints weight = 45955.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074121 restraints weight = 31067.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075546 restraints weight = 27517.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075358 restraints weight = 25006.664| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 39765 Z= 0.198 Angle : 0.620 12.497 53880 Z= 0.321 Chirality : 0.046 0.189 6420 Planarity : 0.005 0.064 6885 Dihedral : 4.681 18.241 5415 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 1.02 % Allowed : 4.47 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4980 helix: 0.68 (0.19), residues: 780 sheet: 1.19 (0.10), residues: 2700 loop : -1.06 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 370 TYR 0.016 0.002 TYR C 195 PHE 0.023 0.002 PHE M 289 TRP 0.017 0.001 TRP L 309 HIS 0.002 0.001 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00466 (39765) covalent geometry : angle 0.62040 (53880) hydrogen bonds : bond 0.04623 ( 2659) hydrogen bonds : angle 4.58951 ( 8394) *********************** 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 184 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9103 (p) REVERT: D 397 ARG cc_start: 0.6498 (mmt90) cc_final: 0.5780 (mtp85) REVERT: F 496 LEU cc_start: 0.9260 (mt) cc_final: 0.8939 (tt) REVERT: H 363 LYS cc_start: 0.8458 (tttt) cc_final: 0.8241 (ttpp) REVERT: I 496 LEU cc_start: 0.9450 (mp) cc_final: 0.9143 (tt) REVERT: J 183 MET cc_start: 0.8486 (mtm) cc_final: 0.7961 (mpp) REVERT: J 447 LEU cc_start: 0.8240 (mt) cc_final: 0.7834 (tt) REVERT: K 496 LEU cc_start: 0.9177 (mp) cc_final: 0.8851 (tt) REVERT: L 363 LYS cc_start: 0.8673 (tttt) cc_final: 0.8431 (ttmm) REVERT: L 496 LEU cc_start: 0.9355 (mt) cc_final: 0.9120 (tt) REVERT: N 341 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7673 (tm-30) REVERT: N 382 ILE cc_start: 0.8765 (mp) cc_final: 0.8510 (mp) REVERT: O 397 ARG cc_start: 0.7309 (mtp85) cc_final: 0.6692 (mtp85) REVERT: O 409 MET cc_start: 0.8697 (ttp) cc_final: 0.8207 (ttp) outliers start: 45 outliers final: 33 residues processed: 174 average time/residue: 0.2230 time to fit residues: 66.8574 Evaluate side-chains 165 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 447 LEU Chi-restraints excluded: chain A residue 513 ILE 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 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 397 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 513 ILE 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 424 MET Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR 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 294 VAL Chi-restraints excluded: chain O residue 389 PHE 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 78 optimal weight: 20.0000 chunk 385 optimal weight: 4.9990 chunk 305 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 363 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 424 optimal weight: 0.8980 chunk 391 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.072728 restraints weight = 74971.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075604 restraints weight = 45164.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076369 restraints weight = 30601.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076604 restraints weight = 26595.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076790 restraints weight = 25783.163| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39765 Z= 0.120 Angle : 0.544 13.569 53880 Z= 0.283 Chirality : 0.045 0.184 6420 Planarity : 0.005 0.062 6885 Dihedral : 4.454 19.879 5415 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.02 % Allowed : 4.47 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4980 helix: 1.08 (0.20), residues: 780 sheet: 1.19 (0.10), residues: 2745 loop : -0.85 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 397 TYR 0.013 0.001 TYR N 499 PHE 0.015 0.001 PHE N 289 TRP 0.008 0.001 TRP E 540 HIS 0.001 0.000 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00266 (39765) covalent geometry : angle 0.54392 (53880) hydrogen bonds : bond 0.03938 ( 2659) hydrogen bonds : angle 4.40548 ( 8394) *********************** 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 182 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9112 (p) REVERT: F 496 LEU cc_start: 0.9344 (mt) cc_final: 0.9063 (tt) REVERT: H 183 MET cc_start: 0.7667 (mtp) cc_final: 0.7461 (mtt) REVERT: I 496 LEU cc_start: 0.9421 (mp) cc_final: 0.9168 (tt) REVERT: J 183 MET cc_start: 0.8469 (mtm) cc_final: 0.7949 (mpp) REVERT: J 447 LEU cc_start: 0.8448 (mt) cc_final: 0.7998 (tt) REVERT: K 397 ARG cc_start: 0.5828 (mmt90) cc_final: 0.5427 (mmm-85) REVERT: K 496 LEU cc_start: 0.9183 (mp) cc_final: 0.8885 (tt) REVERT: L 363 LYS cc_start: 0.8639 (tttt) cc_final: 0.8390 (ttmm) REVERT: L 496 LEU cc_start: 0.9352 (mt) cc_final: 0.9121 (tt) REVERT: N 382 ILE cc_start: 0.8766 (mp) cc_final: 0.8460 (mp) REVERT: O 409 MET cc_start: 0.8629 (ttp) cc_final: 0.8410 (tmm) outliers start: 45 outliers final: 29 residues processed: 173 average time/residue: 0.2182 time to fit residues: 65.2444 Evaluate side-chains 162 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL 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 480 THR 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 D residue 366 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR 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 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 389 PHE 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 35 optimal weight: 3.9990 chunk 166 optimal weight: 0.0170 chunk 282 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 266 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072200 restraints weight = 74681.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075272 restraints weight = 43884.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076098 restraints weight = 28989.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076609 restraints weight = 25781.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076728 restraints weight = 25277.331| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39765 Z= 0.142 Angle : 0.560 11.703 53880 Z= 0.290 Chirality : 0.045 0.188 6420 Planarity : 0.005 0.063 6885 Dihedral : 4.467 20.289 5415 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.20 % Allowed : 4.40 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4980 helix: 1.13 (0.20), residues: 780 sheet: 1.20 (0.10), residues: 2745 loop : -0.84 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 397 TYR 0.012 0.001 TYR N 499 PHE 0.018 0.001 PHE N 289 TRP 0.013 0.001 TRP L 309 HIS 0.002 0.000 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00326 (39765) covalent geometry : angle 0.55965 (53880) hydrogen bonds : bond 0.04097 ( 2659) hydrogen bonds : angle 4.39359 ( 8394) *********************** 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 187 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9112 (p) REVERT: F 496 LEU cc_start: 0.9330 (mt) cc_final: 0.9057 (tt) REVERT: H 397 ARG cc_start: 0.6365 (mtt-85) cc_final: 0.6088 (mtt-85) REVERT: J 183 MET cc_start: 0.8473 (mtm) cc_final: 0.7908 (mpp) REVERT: J 382 ILE cc_start: 0.9159 (mt) cc_final: 0.8926 (mt) REVERT: J 447 LEU cc_start: 0.8469 (mt) cc_final: 0.7984 (tp) REVERT: K 397 ARG cc_start: 0.5862 (mmt90) cc_final: 0.5624 (mmm-85) REVERT: K 496 LEU cc_start: 0.9155 (mp) cc_final: 0.8874 (tt) REVERT: L 363 LYS cc_start: 0.8659 (tttt) cc_final: 0.8401 (ttmm) REVERT: L 496 LEU cc_start: 0.9337 (mt) cc_final: 0.9135 (tt) REVERT: N 382 ILE cc_start: 0.8770 (mp) cc_final: 0.8465 (mp) REVERT: N 424 MET cc_start: 0.8897 (mtm) cc_final: 0.8689 (mtm) REVERT: O 397 ARG cc_start: 0.7198 (mtp85) cc_final: 0.6602 (mtp85) REVERT: O 409 MET cc_start: 0.8586 (ttp) cc_final: 0.8323 (tmm) outliers start: 53 outliers final: 43 residues processed: 179 average time/residue: 0.2259 time to fit residues: 70.3747 Evaluate side-chains 172 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 513 ILE 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 480 THR 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 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 397 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain G residue 294 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 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR 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 513 ILE Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain O residue 461 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 491 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 0.0000 chunk 353 optimal weight: 1.9990 chunk 364 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN G 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072238 restraints weight = 75100.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075477 restraints weight = 44005.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076632 restraints weight = 29928.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.078271 restraints weight = 24063.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077924 restraints weight = 20806.133| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39765 Z= 0.132 Angle : 0.548 11.847 53880 Z= 0.283 Chirality : 0.045 0.188 6420 Planarity : 0.004 0.062 6885 Dihedral : 4.431 20.832 5415 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.09 % Allowed : 4.72 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4980 helix: 1.25 (0.20), residues: 780 sheet: 1.20 (0.10), residues: 2745 loop : -0.82 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 397 TYR 0.012 0.001 TYR N 499 PHE 0.016 0.001 PHE N 289 TRP 0.009 0.001 TRP E 540 HIS 0.002 0.000 HIS O 303 Details of bonding type rmsd covalent geometry : bond 0.00300 (39765) covalent geometry : angle 0.54799 (53880) hydrogen bonds : bond 0.03964 ( 2659) hydrogen bonds : angle 4.34851 ( 8394) *********************** 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 180 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9101 (p) REVERT: D 397 ARG cc_start: 0.5777 (mmt90) cc_final: 0.4822 (mmt90) REVERT: E 424 MET cc_start: 0.8815 (mtm) cc_final: 0.8394 (mpp) REVERT: F 496 LEU cc_start: 0.9284 (mt) cc_final: 0.9047 (tt) REVERT: H 397 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.7096 (mtt-85) REVERT: J 183 MET cc_start: 0.8473 (mtm) cc_final: 0.7905 (mpp) REVERT: J 382 ILE cc_start: 0.9170 (mt) cc_final: 0.8934 (mt) REVERT: J 447 LEU cc_start: 0.8469 (mt) cc_final: 0.7966 (tp) REVERT: K 397 ARG cc_start: 0.6060 (mmt90) cc_final: 0.5378 (mtp85) REVERT: K 496 LEU cc_start: 0.9110 (mp) cc_final: 0.8858 (tt) REVERT: L 363 LYS cc_start: 0.8662 (tttt) cc_final: 0.8393 (ttmm) REVERT: O 409 MET cc_start: 0.8583 (ttp) cc_final: 0.8319 (tmm) outliers start: 48 outliers final: 44 residues processed: 172 average time/residue: 0.2345 time to fit residues: 69.4827 Evaluate side-chains 174 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 447 LEU Chi-restraints excluded: chain A residue 513 ILE 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 C residue 294 VAL 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 D residue 447 LEU 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 397 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain G residue 294 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 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 480 THR 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 L residue 294 VAL Chi-restraints excluded: chain L residue 305 GLU Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR 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 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE 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 103 optimal weight: 3.9990 chunk 451 optimal weight: 2.9990 chunk 396 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 405 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 387 optimal weight: 0.5980 chunk 312 optimal weight: 0.2980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN E 200 GLN G 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070599 restraints weight = 75155.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073801 restraints weight = 44080.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075093 restraints weight = 29906.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075898 restraints weight = 24002.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075779 restraints weight = 22467.962| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39765 Z= 0.196 Angle : 0.612 15.004 53880 Z= 0.315 Chirality : 0.046 0.215 6420 Planarity : 0.005 0.065 6885 Dihedral : 4.625 23.547 5415 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.13 % Allowed : 4.65 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4980 helix: 1.00 (0.19), residues: 780 sheet: 1.17 (0.10), residues: 2715 loop : -0.86 (0.18), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 370 TYR 0.015 0.002 TYR C 195 PHE 0.020 0.002 PHE G 289 TRP 0.019 0.001 TRP L 309 HIS 0.003 0.001 HIS G 403 Details of bonding type rmsd covalent geometry : bond 0.00464 (39765) covalent geometry : angle 0.61162 (53880) hydrogen bonds : bond 0.04494 ( 2659) hydrogen bonds : angle 4.50885 ( 8394) ********************** 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 183 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9093 (p) REVERT: D 397 ARG cc_start: 0.6473 (mmt90) cc_final: 0.5580 (mmt90) REVERT: F 496 LEU cc_start: 0.9300 (mt) cc_final: 0.9045 (tt) REVERT: J 183 MET cc_start: 0.8494 (mtm) cc_final: 0.7921 (mpp) REVERT: J 447 LEU cc_start: 0.8547 (mt) cc_final: 0.7992 (tt) REVERT: K 496 LEU cc_start: 0.9124 (mp) cc_final: 0.8877 (tt) REVERT: L 363 LYS cc_start: 0.8692 (tttt) cc_final: 0.8436 (ttmm) REVERT: O 409 MET cc_start: 0.8664 (ttp) cc_final: 0.8187 (ttp) outliers start: 50 outliers final: 44 residues processed: 174 average time/residue: 0.2324 time to fit residues: 69.7638 Evaluate side-chains 172 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 513 ILE 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 510 VAL Chi-restraints excluded: chain C residue 294 VAL 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 183 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 294 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 294 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 480 THR 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 L residue 294 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 510 VAL Chi-restraints excluded: chain N residue 512 MET Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain O residue 461 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 389 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 398 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 GLN I 506 ASN N 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.064825 restraints weight = 77448.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.067672 restraints weight = 40957.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.069468 restraints weight = 28054.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070572 restraints weight = 22400.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071243 restraints weight = 19604.651| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 39765 Z= 0.234 Angle : 0.664 13.248 53880 Z= 0.339 Chirality : 0.046 0.203 6420 Planarity : 0.005 0.065 6885 Dihedral : 4.840 25.801 5415 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 4.81 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4980 helix: 0.79 (0.19), residues: 780 sheet: 1.08 (0.10), residues: 2715 loop : -0.92 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 370 TYR 0.018 0.002 TYR C 195 PHE 0.021 0.002 PHE M 511 TRP 0.022 0.002 TRP L 309 HIS 0.003 0.001 HIS G 403 Details of bonding type rmsd covalent geometry : bond 0.00557 (39765) covalent geometry : angle 0.66410 (53880) hydrogen bonds : bond 0.04789 ( 2659) hydrogen bonds : angle 4.64976 ( 8394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.79 seconds wall clock time: 84 minutes 8.69 seconds (5048.69 seconds total)