Starting phenix.real_space_refine on Sun Feb 18 02:06:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/02_2024/7f5t_31466.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 112 5.16 5 C 12800 2.51 5 N 3620 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ASP 548": "OD1" <-> "OD2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ASP 690": "OD1" <-> "OD2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ASP 548": "OD1" <-> "OD2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C ASP 690": "OD1" <-> "OD2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ASP 548": "OD1" <-> "OD2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ASP 690": "OD1" <-> "OD2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "B GLU 801": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 10.47, per 1000 atoms: 0.51 Number of scatterers: 20436 At special positions: 0 Unit cell: (193.98, 107.06, 94.34, 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 112 16.00 O 3904 8.00 N 3620 7.00 C 12800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.29 Conformation dependent library (CDL) restraints added in 5.0 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 20 sheets defined 51.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 349 through 363 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 512 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.763A pdb=" N TYR C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 180' Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.852A pdb=" N SER C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.777A pdb=" N ILE C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 433 Processing helix chain 'C' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 512 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 609 through 612 Processing helix chain 'C' and resid 614 through 627 Processing helix chain 'C' and resid 633 through 640 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 716 through 720 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 95 removed outlier: 4.125A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 180 " --> pdb=" O PRO D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 415 through 433 Processing helix chain 'D' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 512 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 614 through 627 Processing helix chain 'D' and resid 633 through 640 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 716 through 720 Processing helix chain 'D' and resid 740 through 744 Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG A 58 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE A 250 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 336 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL C 705 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP A 748 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS C 707 " --> pdb=" O TRP A 748 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 750 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP C 683 " --> pdb=" O PHE C 706 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 572 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 607 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE C 574 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 604 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 664 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE C 606 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU A 604 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 664 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A 572 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS A 607 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 683 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 751 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 451 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 442 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG B 58 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE B 250 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 336 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 173 removed outlier: 3.932A pdb=" N ALA B 169 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG B 442 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL D 705 " --> pdb=" O THR B 746 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP B 748 " --> pdb=" O VAL D 705 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS D 707 " --> pdb=" O TRP B 748 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 750 " --> pdb=" O HIS D 707 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 683 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 572 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS D 607 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 574 " --> pdb=" O HIS D 607 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 604 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL D 664 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 606 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.645A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU B 604 " --> pdb=" O GLU B 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 664 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS B 607 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 683 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 751 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 451 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 442 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG C 58 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 250 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 336 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU C 462 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 461 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 542 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY C 726 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.841A pdb=" N ARG D 58 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 250 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 336 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA D 169 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU D 462 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 461 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 542 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY D 726 " --> pdb=" O VAL D 738 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2724 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: 7.88 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6350 1.33 - 1.45: 2720 1.45 - 1.57: 11474 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 20728 Sorted by residual: bond pdb=" CA LEU B 53 " pdb=" C LEU B 53 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.56e-02 4.11e+03 1.29e+01 bond pdb=" CA LEU D 53 " pdb=" C LEU D 53 " ideal model delta sigma weight residual 1.523 1.468 0.056 1.56e-02 4.11e+03 1.27e+01 bond pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.25e+01 bond pdb=" CA LEU C 53 " pdb=" C LEU C 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" CA VAL D 346 " pdb=" CB VAL D 346 " ideal model delta sigma weight residual 1.540 1.517 0.023 7.70e-03 1.69e+04 8.74e+00 ... (remaining 20723 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.66: 555 106.66 - 113.49: 12228 113.49 - 120.32: 7169 120.32 - 127.15: 7896 127.15 - 133.98: 188 Bond angle restraints: 28036 Sorted by residual: angle pdb=" C ALA D 345 " pdb=" N VAL D 346 " pdb=" CA VAL D 346 " ideal model delta sigma weight residual 123.33 118.63 4.70 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA C 345 " pdb=" N VAL C 346 " pdb=" CA VAL C 346 " ideal model delta sigma weight residual 123.33 118.64 4.69 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA A 345 " pdb=" N VAL A 346 " pdb=" CA VAL A 346 " ideal model delta sigma weight residual 123.33 118.65 4.68 8.70e-01 1.32e+00 2.90e+01 angle pdb=" C ALA B 345 " pdb=" N VAL B 346 " pdb=" CA VAL B 346 " ideal model delta sigma weight residual 123.33 118.67 4.66 8.70e-01 1.32e+00 2.87e+01 angle pdb=" N ALA A 691 " pdb=" CA ALA A 691 " pdb=" C ALA A 691 " ideal model delta sigma weight residual 111.03 105.16 5.87 1.11e+00 8.12e-01 2.80e+01 ... (remaining 28031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11333 17.73 - 35.45: 1040 35.45 - 53.18: 243 53.18 - 70.90: 36 70.90 - 88.63: 28 Dihedral angle restraints: 12680 sinusoidal: 4932 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ASN B 344 " pdb=" C ASN B 344 " pdb=" N ALA B 345 " pdb=" CA ALA B 345 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASN A 344 " pdb=" C ASN A 344 " pdb=" N ALA A 345 " pdb=" CA ALA A 345 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASN C 344 " pdb=" C ASN C 344 " pdb=" N ALA C 345 " pdb=" CA ALA C 345 " ideal model delta harmonic sigma weight residual 180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2196 0.038 - 0.076: 793 0.076 - 0.113: 277 0.113 - 0.151: 34 0.151 - 0.189: 8 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA LEU B 53 " pdb=" N LEU B 53 " pdb=" C LEU B 53 " pdb=" CB LEU B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA LEU D 53 " pdb=" N LEU D 53 " pdb=" C LEU D 53 " pdb=" CB LEU D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA LEU C 53 " pdb=" N LEU C 53 " pdb=" C LEU C 53 " pdb=" CB LEU C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3305 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 597 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ALA B 597 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 597 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 598 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 597 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ALA C 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA C 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS C 598 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 597 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ALA A 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 598 " -0.011 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1288 2.69 - 3.24: 24453 3.24 - 3.80: 34306 3.80 - 4.35: 41978 4.35 - 4.90: 66489 Nonbonded interactions: 168514 Sorted by model distance: nonbonded pdb=" O ASN D 354 " pdb=" OG1 THR D 357 " model vdw 2.141 2.440 nonbonded pdb=" O ASN A 354 " pdb=" OG1 THR A 357 " model vdw 2.141 2.440 nonbonded pdb=" O ASN B 354 " pdb=" OG1 THR B 357 " model vdw 2.142 2.440 nonbonded pdb=" O ASN C 354 " pdb=" OG1 THR C 357 " model vdw 2.142 2.440 nonbonded pdb=" O ALA C 399 " pdb=" OG SER C 402 " model vdw 2.204 2.440 ... (remaining 168509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.010 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: 0.010 Extract box with map and model: 6.740 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 59.570 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20728 Z= 0.483 Angle : 0.886 7.118 28036 Z= 0.535 Chirality : 0.043 0.189 3308 Planarity : 0.004 0.041 3632 Dihedral : 15.070 88.631 7656 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.25 % Favored : 86.30 % Rotamer: Outliers : 3.48 % Allowed : 7.14 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.13), residues: 2664 helix: -2.50 (0.12), residues: 1136 sheet: -4.18 (0.18), residues: 428 loop : -3.78 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 304 HIS 0.008 0.002 HIS A 272 PHE 0.018 0.002 PHE B 642 TYR 0.017 0.002 TYR B 55 ARG 0.006 0.001 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 275 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8693 (tp) cc_final: 0.7658 (tt) REVERT: A 178 PHE cc_start: 0.8419 (m-80) cc_final: 0.8190 (m-80) REVERT: A 209 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8823 (p) REVERT: A 503 MET cc_start: 0.8674 (tpt) cc_final: 0.8435 (tpp) REVERT: B 209 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 503 MET cc_start: 0.8601 (tpt) cc_final: 0.8398 (tpp) REVERT: C 153 LEU cc_start: 0.8702 (tp) cc_final: 0.7603 (tt) REVERT: C 154 MET cc_start: 0.7740 (mmm) cc_final: 0.7230 (tpp) REVERT: C 158 ASP cc_start: 0.8234 (m-30) cc_final: 0.7484 (m-30) REVERT: C 178 PHE cc_start: 0.8456 (m-80) cc_final: 0.8175 (m-80) REVERT: C 209 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 240 LEU cc_start: 0.9492 (tt) cc_final: 0.9283 (tp) REVERT: C 503 MET cc_start: 0.8679 (tpt) cc_final: 0.8466 (tpp) REVERT: D 178 PHE cc_start: 0.8579 (m-80) cc_final: 0.8287 (m-80) REVERT: D 209 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8625 (p) REVERT: D 240 LEU cc_start: 0.9506 (tt) cc_final: 0.9302 (tp) REVERT: D 503 MET cc_start: 0.8621 (tpt) cc_final: 0.8384 (tpp) outliers start: 76 outliers final: 19 residues processed: 329 average time/residue: 0.3654 time to fit residues: 181.7342 Evaluate side-chains 216 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 3.9990 chunk 203 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 363 GLN A 369 GLN A 607 HIS A 652 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 369 GLN B 607 HIS B 652 HIS C 150 GLN C 363 GLN C 369 GLN C 607 HIS C 652 HIS D 150 GLN D 363 GLN D 369 GLN D 607 HIS D 652 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20728 Z= 0.172 Angle : 0.620 10.044 28036 Z= 0.319 Chirality : 0.043 0.233 3308 Planarity : 0.004 0.045 3632 Dihedral : 5.229 28.497 2872 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.83 % Favored : 92.87 % Rotamer: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.15), residues: 2664 helix: -0.55 (0.15), residues: 1184 sheet: -3.14 (0.21), residues: 428 loop : -2.98 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 304 HIS 0.005 0.001 HIS C 74 PHE 0.010 0.001 PHE A 696 TYR 0.037 0.001 TYR C 157 ARG 0.007 0.000 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8774 (tp) cc_final: 0.8555 (tp) REVERT: A 503 MET cc_start: 0.8539 (tpt) cc_final: 0.8312 (tpp) REVERT: B 113 LEU cc_start: 0.9235 (mt) cc_final: 0.8995 (tp) REVERT: B 119 MET cc_start: 0.9379 (mmm) cc_final: 0.9089 (mmm) REVERT: B 271 MET cc_start: 0.8923 (ptp) cc_final: 0.8512 (ptp) REVERT: B 503 MET cc_start: 0.8542 (tpt) cc_final: 0.8232 (tpp) REVERT: C 271 MET cc_start: 0.8982 (ptp) cc_final: 0.8532 (ptp) REVERT: C 503 MET cc_start: 0.8550 (tpt) cc_final: 0.8294 (tpp) REVERT: D 113 LEU cc_start: 0.9109 (mt) cc_final: 0.8858 (tp) REVERT: D 271 MET cc_start: 0.8896 (ptp) cc_final: 0.8595 (ptp) REVERT: D 503 MET cc_start: 0.8550 (tpt) cc_final: 0.8217 (tpp) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.3407 time to fit residues: 141.4339 Evaluate side-chains 191 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 30.0000 chunk 243 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 241 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 204 ASN A 392 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 HIS A 708 ASN B 185 ASN ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 392 ASN ** C 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20728 Z= 0.328 Angle : 0.681 9.206 28036 Z= 0.361 Chirality : 0.043 0.158 3308 Planarity : 0.005 0.062 3632 Dihedral : 5.425 32.141 2872 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.22 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2664 helix: -0.17 (0.15), residues: 1180 sheet: -2.90 (0.19), residues: 476 loop : -2.97 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 304 HIS 0.006 0.002 HIS A 707 PHE 0.020 0.002 PHE D 161 TYR 0.024 0.003 TYR A 157 ARG 0.019 0.001 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.9009 (ptp) cc_final: 0.8689 (ptp) REVERT: A 488 LEU cc_start: 0.8864 (tp) cc_final: 0.8590 (tp) REVERT: A 503 MET cc_start: 0.8605 (tpt) cc_final: 0.8395 (tpp) REVERT: B 119 MET cc_start: 0.9328 (mmm) cc_final: 0.8995 (mmm) REVERT: B 271 MET cc_start: 0.9047 (ptp) cc_final: 0.8765 (ptp) REVERT: B 488 LEU cc_start: 0.9011 (tp) cc_final: 0.8741 (tp) REVERT: B 503 MET cc_start: 0.8609 (tpt) cc_final: 0.8353 (tpp) REVERT: C 271 MET cc_start: 0.9055 (ptp) cc_final: 0.8790 (ptp) REVERT: C 488 LEU cc_start: 0.8959 (tp) cc_final: 0.8696 (tp) REVERT: C 503 MET cc_start: 0.8605 (tpt) cc_final: 0.8382 (tpp) REVERT: D 119 MET cc_start: 0.9492 (mmp) cc_final: 0.9024 (mmp) REVERT: D 488 LEU cc_start: 0.8975 (tp) cc_final: 0.8722 (tp) REVERT: D 503 MET cc_start: 0.8568 (tpt) cc_final: 0.8321 (tpp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3548 time to fit residues: 116.3644 Evaluate side-chains 163 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 26 optimal weight: 0.0370 chunk 116 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 overall best weight: 3.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 637 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 HIS C 637 ASN C 707 HIS D 637 ASN D 707 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20728 Z= 0.194 Angle : 0.590 11.912 28036 Z= 0.304 Chirality : 0.042 0.252 3308 Planarity : 0.004 0.050 3632 Dihedral : 5.035 30.761 2872 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.91 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2664 helix: 0.46 (0.15), residues: 1196 sheet: -2.33 (0.21), residues: 472 loop : -2.63 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 748 HIS 0.005 0.001 HIS B 559 PHE 0.009 0.001 PHE C 466 TYR 0.020 0.002 TYR C 157 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.9110 (ptp) cc_final: 0.8746 (ptp) REVERT: A 488 LEU cc_start: 0.9016 (tp) cc_final: 0.8776 (tp) REVERT: A 503 MET cc_start: 0.8519 (tpt) cc_final: 0.8274 (tpp) REVERT: B 113 LEU cc_start: 0.9195 (mt) cc_final: 0.8907 (tp) REVERT: B 119 MET cc_start: 0.9381 (mmm) cc_final: 0.9024 (mmm) REVERT: B 488 LEU cc_start: 0.9046 (tp) cc_final: 0.8814 (tp) REVERT: B 503 MET cc_start: 0.8576 (tpt) cc_final: 0.8294 (tpp) REVERT: C 488 LEU cc_start: 0.9069 (tp) cc_final: 0.8837 (tp) REVERT: C 503 MET cc_start: 0.8536 (tpt) cc_final: 0.8240 (tpp) REVERT: D 113 LEU cc_start: 0.9050 (mt) cc_final: 0.8819 (tt) REVERT: D 119 MET cc_start: 0.9516 (mmp) cc_final: 0.9070 (mmp) REVERT: D 271 MET cc_start: 0.9007 (ptp) cc_final: 0.8646 (ptp) REVERT: D 488 LEU cc_start: 0.9053 (tp) cc_final: 0.8816 (tp) REVERT: D 503 MET cc_start: 0.8575 (tpt) cc_final: 0.8270 (tpp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3249 time to fit residues: 105.3953 Evaluate side-chains 168 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 232 optimal weight: 0.8980 chunk 65 optimal weight: 50.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 454 GLN B 637 ASN C 392 ASN C 454 GLN D 454 GLN D 499 ASN D 559 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20728 Z= 0.249 Angle : 0.626 8.936 28036 Z= 0.323 Chirality : 0.042 0.175 3308 Planarity : 0.004 0.057 3632 Dihedral : 5.121 31.053 2872 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.66 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2664 helix: 0.64 (0.15), residues: 1192 sheet: -1.95 (0.21), residues: 468 loop : -2.62 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 304 HIS 0.005 0.001 HIS C 707 PHE 0.020 0.002 PHE B 161 TYR 0.015 0.002 TYR A 573 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9133 (tp) cc_final: 0.8910 (tp) REVERT: A 503 MET cc_start: 0.8532 (tpt) cc_final: 0.8290 (tpp) REVERT: B 119 MET cc_start: 0.9376 (mmm) cc_final: 0.9024 (mmm) REVERT: B 271 MET cc_start: 0.9066 (ptp) cc_final: 0.8838 (ptp) REVERT: B 488 LEU cc_start: 0.9070 (tp) cc_final: 0.8838 (tp) REVERT: B 503 MET cc_start: 0.8568 (tpt) cc_final: 0.8310 (tpp) REVERT: C 271 MET cc_start: 0.9050 (ptp) cc_final: 0.8838 (ptp) REVERT: C 488 LEU cc_start: 0.9109 (tp) cc_final: 0.8887 (tp) REVERT: C 503 MET cc_start: 0.8561 (tpt) cc_final: 0.8287 (tpp) REVERT: D 119 MET cc_start: 0.9499 (mmp) cc_final: 0.9091 (mmp) REVERT: D 271 MET cc_start: 0.9026 (ptp) cc_final: 0.8715 (ptp) REVERT: D 503 MET cc_start: 0.8557 (tpt) cc_final: 0.8297 (tpp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.3196 time to fit residues: 101.6435 Evaluate side-chains 153 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 559 HIS A 708 ASN B 454 GLN B 556 GLN C 392 ASN C 559 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.004 0.037 20728 Z= 0.252 Angle : 0.621 10.593 28036 Z= 0.323 Chirality : 0.042 0.173 3308 Planarity : 0.004 0.061 3632 Dihedral : 5.157 31.126 2872 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.92 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2664 helix: 0.67 (0.15), residues: 1192 sheet: -1.68 (0.22), residues: 468 loop : -2.35 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 304 HIS 0.004 0.001 HIS C 74 PHE 0.031 0.002 PHE C 161 TYR 0.016 0.002 TYR A 157 ARG 0.007 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9119 (tp) cc_final: 0.8875 (tp) REVERT: A 503 MET cc_start: 0.8537 (tpt) cc_final: 0.8297 (tpp) REVERT: B 119 MET cc_start: 0.9329 (mmm) cc_final: 0.9007 (mmm) REVERT: B 271 MET cc_start: 0.9070 (ptp) cc_final: 0.8727 (ptp) REVERT: B 488 LEU cc_start: 0.9058 (tp) cc_final: 0.8836 (tp) REVERT: B 503 MET cc_start: 0.8558 (tpt) cc_final: 0.8311 (tpp) REVERT: C 271 MET cc_start: 0.9084 (ptp) cc_final: 0.8744 (ptp) REVERT: C 488 LEU cc_start: 0.9120 (tp) cc_final: 0.8904 (tp) REVERT: C 503 MET cc_start: 0.8548 (tpt) cc_final: 0.8289 (tpp) REVERT: D 119 MET cc_start: 0.9489 (mmp) cc_final: 0.9093 (mmp) REVERT: D 503 MET cc_start: 0.8575 (tpt) cc_final: 0.8341 (tpp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3221 time to fit residues: 99.1907 Evaluate side-chains 152 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 218 optimal weight: 30.0000 chunk 144 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 556 GLN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20728 Z= 0.215 Angle : 0.591 8.309 28036 Z= 0.303 Chirality : 0.041 0.158 3308 Planarity : 0.004 0.067 3632 Dihedral : 5.009 31.466 2872 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.06 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2664 helix: 0.87 (0.15), residues: 1204 sheet: -1.45 (0.23), residues: 468 loop : -2.34 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 264 HIS 0.003 0.001 HIS C 74 PHE 0.033 0.002 PHE A 161 TYR 0.012 0.002 TYR A 573 ARG 0.008 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9125 (tp) cc_final: 0.8906 (tp) REVERT: A 503 MET cc_start: 0.8521 (tpt) cc_final: 0.8293 (tpp) REVERT: B 119 MET cc_start: 0.9291 (mmm) cc_final: 0.8983 (mmm) REVERT: B 271 MET cc_start: 0.9026 (ptp) cc_final: 0.8693 (ptp) REVERT: B 488 LEU cc_start: 0.9080 (tp) cc_final: 0.8848 (tp) REVERT: B 503 MET cc_start: 0.8555 (tpt) cc_final: 0.8325 (tpp) REVERT: C 167 LYS cc_start: 0.8210 (mppt) cc_final: 0.7991 (mmtm) REVERT: C 271 MET cc_start: 0.9038 (ptp) cc_final: 0.8705 (ptp) REVERT: C 503 MET cc_start: 0.8535 (tpt) cc_final: 0.8273 (tpp) REVERT: D 119 MET cc_start: 0.9461 (mmp) cc_final: 0.9107 (mmp) REVERT: D 503 MET cc_start: 0.8549 (tpt) cc_final: 0.8315 (tpp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3293 time to fit residues: 103.4515 Evaluate side-chains 158 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 203 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 overall best weight: 3.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 556 GLN C 392 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20728 Z= 0.187 Angle : 0.592 9.776 28036 Z= 0.300 Chirality : 0.042 0.283 3308 Planarity : 0.004 0.056 3632 Dihedral : 4.870 31.207 2872 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2664 helix: 0.96 (0.15), residues: 1208 sheet: -1.14 (0.24), residues: 460 loop : -2.30 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 264 HIS 0.003 0.001 HIS B 74 PHE 0.030 0.002 PHE B 161 TYR 0.010 0.001 TYR A 573 ARG 0.012 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9129 (tp) cc_final: 0.8922 (tp) REVERT: A 503 MET cc_start: 0.8527 (tpt) cc_final: 0.8192 (tpp) REVERT: B 119 MET cc_start: 0.9288 (mmm) cc_final: 0.8992 (mmm) REVERT: B 271 MET cc_start: 0.9014 (ptp) cc_final: 0.8713 (ptp) REVERT: B 488 LEU cc_start: 0.9088 (tp) cc_final: 0.8870 (tp) REVERT: B 503 MET cc_start: 0.8534 (tpt) cc_final: 0.8303 (tpp) REVERT: C 271 MET cc_start: 0.9023 (ptp) cc_final: 0.8720 (ptp) REVERT: C 488 LEU cc_start: 0.9083 (tp) cc_final: 0.8879 (tp) REVERT: C 503 MET cc_start: 0.8527 (tpt) cc_final: 0.8216 (tpp) REVERT: D 119 MET cc_start: 0.9452 (mmp) cc_final: 0.9106 (mmp) REVERT: D 503 MET cc_start: 0.8542 (tpt) cc_final: 0.8283 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3184 time to fit residues: 101.4651 Evaluate side-chains 161 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 30.0000 chunk 225 optimal weight: 50.0000 chunk 240 optimal weight: 10.0000 chunk 144 optimal weight: 0.0670 chunk 104 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 overall best weight: 3.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 556 GLN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20728 Z= 0.182 Angle : 0.592 8.476 28036 Z= 0.300 Chirality : 0.043 0.302 3308 Planarity : 0.004 0.057 3632 Dihedral : 4.790 31.573 2872 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.83 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2664 helix: 0.96 (0.15), residues: 1228 sheet: -0.94 (0.24), residues: 460 loop : -2.37 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 264 HIS 0.003 0.001 HIS B 755 PHE 0.024 0.002 PHE A 161 TYR 0.015 0.001 TYR B 157 ARG 0.010 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8765 (ppp) cc_final: 0.8437 (ppp) REVERT: A 503 MET cc_start: 0.8488 (tpt) cc_final: 0.8156 (tpp) REVERT: B 119 MET cc_start: 0.9280 (mmm) cc_final: 0.8990 (mmm) REVERT: B 271 MET cc_start: 0.9000 (ptp) cc_final: 0.8688 (ptp) REVERT: B 503 MET cc_start: 0.8536 (tpt) cc_final: 0.8287 (tpp) REVERT: C 271 MET cc_start: 0.8992 (ptp) cc_final: 0.8679 (ptp) REVERT: C 503 MET cc_start: 0.8545 (tpt) cc_final: 0.8216 (tpp) REVERT: D 119 MET cc_start: 0.9397 (mmp) cc_final: 0.9109 (mmm) REVERT: D 488 LEU cc_start: 0.8904 (tp) cc_final: 0.8670 (tt) REVERT: D 503 MET cc_start: 0.8548 (tpt) cc_final: 0.8270 (tpp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3361 time to fit residues: 107.7524 Evaluate side-chains 154 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 40.0000 chunk 245 optimal weight: 2.9990 chunk 212 optimal weight: 0.0170 chunk 22 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 556 GLN C 392 ASN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20728 Z= 0.179 Angle : 0.588 9.545 28036 Z= 0.297 Chirality : 0.042 0.280 3308 Planarity : 0.004 0.057 3632 Dihedral : 4.752 31.746 2872 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.91 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2664 helix: 1.01 (0.15), residues: 1228 sheet: -0.81 (0.25), residues: 460 loop : -2.30 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 264 HIS 0.004 0.001 HIS B 74 PHE 0.028 0.002 PHE D 161 TYR 0.013 0.001 TYR B 157 ARG 0.010 0.000 ARG B 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8677 (ppp) cc_final: 0.8312 (ppp) REVERT: A 503 MET cc_start: 0.8525 (tpt) cc_final: 0.8191 (tpp) REVERT: B 119 MET cc_start: 0.9271 (mmm) cc_final: 0.8996 (mmm) REVERT: B 259 TYR cc_start: 0.8268 (m-80) cc_final: 0.8034 (m-80) REVERT: B 488 LEU cc_start: 0.9110 (tp) cc_final: 0.8908 (tp) REVERT: B 503 MET cc_start: 0.8538 (tpt) cc_final: 0.8221 (tpp) REVERT: C 503 MET cc_start: 0.8531 (tpt) cc_final: 0.8189 (tpp) REVERT: D 119 MET cc_start: 0.9407 (mmp) cc_final: 0.9092 (mmm) REVERT: D 271 MET cc_start: 0.8582 (ppp) cc_final: 0.8241 (ppp) REVERT: D 503 MET cc_start: 0.8554 (tpt) cc_final: 0.8258 (tpp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3171 time to fit residues: 102.4123 Evaluate side-chains 158 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 212 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 556 GLN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.042653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033331 restraints weight = 183144.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034048 restraints weight = 132994.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.034643 restraints weight = 105283.208| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20728 Z= 0.163 Angle : 0.579 8.837 28036 Z= 0.289 Chirality : 0.042 0.278 3308 Planarity : 0.004 0.057 3632 Dihedral : 4.624 29.990 2872 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2664 helix: 1.08 (0.15), residues: 1236 sheet: -0.67 (0.25), residues: 460 loop : -2.18 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 264 HIS 0.004 0.001 HIS D 74 PHE 0.018 0.001 PHE B 161 TYR 0.018 0.001 TYR D 157 ARG 0.009 0.000 ARG B 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.98 seconds wall clock time: 64 minutes 35.93 seconds (3875.93 seconds total)