Starting phenix.real_space_refine on Mon Mar 18 08:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q13_13753/03_2024/7q13_13753_updated.pdb" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 108 5.16 5 C 12996 2.51 5 N 3500 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 562": "OD1" <-> "OD2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 562": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20368 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "H" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "C" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "D" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 GLC A 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC A 803 " occ=0.50 residue: pdb=" C1 GLC B 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC B 803 " occ=0.50 residue: pdb=" C1 GLC C 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC C 803 " occ=0.50 residue: pdb=" C1 GLC D 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC D 803 " occ=0.50 Time building chain proxies: 18.50, per 1000 atoms: 0.91 Number of scatterers: 20368 At special positions: 0 Unit cell: (113.42, 137.8, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 12 15.00 O 3752 8.00 N 3500 7.00 C 12996 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: 7.44 Conformation dependent library (CDL) restraints added in 7.0 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 45.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.589A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 146 through 168 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 377 through 410 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 579 through 596 removed outlier: 3.806A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 338 through 348 removed outlier: 4.041A pdb=" N ASP E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 338 through 348 removed outlier: 4.040A pdb=" N ASP F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 327 Processing helix chain 'G' and resid 338 through 348 removed outlier: 4.041A pdb=" N ASP G 346 " --> pdb=" O LYS G 342 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR G 347 " --> pdb=" O ARG G 343 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 327 Processing helix chain 'H' and resid 338 through 348 removed outlier: 4.041A pdb=" N ASP H 346 " --> pdb=" O LYS H 342 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR H 347 " --> pdb=" O ARG H 343 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.589A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 146 through 168 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 292 through 311 Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 340 through 355 Processing helix chain 'B' and resid 377 through 410 Processing helix chain 'B' and resid 422 through 434 Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 560 through 576 Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.806A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'C' and resid 44 through 56 removed outlier: 4.589A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 146 through 168 Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 229 through 232 No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 292 through 311 Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 377 through 410 Processing helix chain 'C' and resid 422 through 434 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 560 through 576 Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.806A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 601 No H-bonds generated for 'chain 'C' and resid 598 through 601' Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'D' and resid 44 through 56 removed outlier: 4.590A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 292 through 311 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 340 through 355 Processing helix chain 'D' and resid 377 through 410 Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'D' and resid 455 through 462 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 560 through 576 Processing helix chain 'D' and resid 579 through 596 removed outlier: 3.806A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 601 No H-bonds generated for 'chain 'D' and resid 598 through 601' Processing helix chain 'D' and resid 603 through 616 Processing sheet with id= A, first strand: chain 'A' and resid 254 through 257 removed outlier: 5.801A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS A 180 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 32 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE A 63 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 113 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY A 66 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 115 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.829A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 504 No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.913A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 254 through 257 removed outlier: 5.801A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS B 180 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL B 32 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE B 63 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 113 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY B 66 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 115 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.829A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 502 through 504 No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 372 through 375 removed outlier: 6.914A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 254 through 257 removed outlier: 5.801A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS C 180 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 32 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE C 63 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 113 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY C 66 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 115 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 323 through 328 removed outlier: 6.828A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 502 through 504 No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 372 through 375 removed outlier: 6.913A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 254 through 257 removed outlier: 5.801A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS D 180 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 32 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 63 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU D 113 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY D 66 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 115 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 323 through 328 removed outlier: 6.829A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 502 through 504 No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 372 through 375 removed outlier: 6.914A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2300 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: 6.29 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6580 1.34 - 1.46: 5064 1.46 - 1.58: 9072 1.58 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 20896 Sorted by residual: bond pdb=" N3 UDP C 802 " pdb=" C4 UDP C 802 " ideal model delta sigma weight residual 1.383 1.331 0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" N3 UDP A 802 " pdb=" C4 UDP A 802 " ideal model delta sigma weight residual 1.383 1.331 0.052 1.20e-02 6.94e+03 1.85e+01 bond pdb=" N3 UDP D 802 " pdb=" C4 UDP D 802 " ideal model delta sigma weight residual 1.383 1.332 0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" N3 UDP B 802 " pdb=" C4 UDP B 802 " ideal model delta sigma weight residual 1.383 1.332 0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" N1 UDP C 802 " pdb=" C6 UDP C 802 " ideal model delta sigma weight residual 1.375 1.334 0.041 1.00e-02 1.00e+04 1.65e+01 ... (remaining 20891 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.87: 580 106.87 - 113.66: 11229 113.66 - 120.45: 8204 120.45 - 127.24: 8064 127.24 - 134.03: 251 Bond angle restraints: 28328 Sorted by residual: angle pdb=" O3A UDP C 802 " pdb=" PB UDP C 802 " pdb=" O3B UDP C 802 " ideal model delta sigma weight residual 112.01 102.80 9.21 1.00e+00 1.00e+00 8.48e+01 angle pdb=" O3A UDP B 802 " pdb=" PB UDP B 802 " pdb=" O3B UDP B 802 " ideal model delta sigma weight residual 112.01 102.84 9.17 1.00e+00 1.00e+00 8.41e+01 angle pdb=" O3A UDP A 802 " pdb=" PB UDP A 802 " pdb=" O3B UDP A 802 " ideal model delta sigma weight residual 112.01 102.84 9.17 1.00e+00 1.00e+00 8.40e+01 angle pdb=" O3A UDP D 802 " pdb=" PB UDP D 802 " pdb=" O3B UDP D 802 " ideal model delta sigma weight residual 112.01 102.85 9.16 1.00e+00 1.00e+00 8.39e+01 angle pdb=" C2 UDP D 802 " pdb=" N3 UDP D 802 " pdb=" C4 UDP D 802 " ideal model delta sigma weight residual 126.93 120.14 6.79 1.00e+00 1.00e+00 4.61e+01 ... (remaining 28323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.57: 11835 29.57 - 59.14: 527 59.14 - 88.72: 57 88.72 - 118.29: 49 118.29 - 147.86: 28 Dihedral angle restraints: 12496 sinusoidal: 5240 harmonic: 7256 Sorted by residual: dihedral pdb=" C3 G6P C 801 " pdb=" C1 G6P C 801 " pdb=" C2 G6P C 801 " pdb=" O1 G6P C 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.21 147.86 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.18 147.83 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C3 G6P A 801 " pdb=" C1 G6P A 801 " pdb=" C2 G6P A 801 " pdb=" O1 G6P A 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.18 147.83 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 12493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 3024 1.020 - 2.039: 0 2.039 - 3.059: 0 3.059 - 4.078: 0 4.078 - 5.098: 16 Chirality restraints: 3040 Sorted by residual: chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C5 G6P D 801 " pdb=" C4 G6P D 801 " pdb=" C6 G6P D 801 " pdb=" O5 G6P D 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 3037 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " 0.020 2.00e-02 2.50e+03 1.85e-02 8.53e+00 pdb=" CG TRP A 106 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 106 " 0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP D 106 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 106 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 106 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 106 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 106 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 106 " -0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 106 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP C 106 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 106 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 106 " -0.001 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2184 2.75 - 3.28: 20418 3.28 - 3.82: 35089 3.82 - 4.36: 42408 4.36 - 4.90: 71055 Nonbonded interactions: 171154 Sorted by model distance: nonbonded pdb=" OE2 GLU B 406 " pdb=" NH2 ARG C 309 " model vdw 2.208 2.520 nonbonded pdb=" OE2 GLU B 292 " pdb=" O3 G6P D 801 " model vdw 2.224 2.440 nonbonded pdb=" OE2 GLU A 292 " pdb=" O3 G6P C 801 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU D 292 " pdb=" O3 G6P B 801 " model vdw 2.231 2.440 nonbonded pdb=" OE2 GLU C 292 " pdb=" O3 G6P A 801 " model vdw 2.270 2.440 ... (remaining 171149 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' and (resid 29 through 587 or resid 589 through 618 or resid 801 throu \ gh 803)) selection = (chain 'B' and (resid 29 through 587 or resid 589 through 618 or resid 801 throu \ gh 803)) selection = (chain 'C' and (resid 29 through 587 or resid 589 through 618 or resid 801 throu \ gh 803)) selection = (chain 'D' and (resid 29 through 587 or resid 589 through 618 or resid 801 throu \ gh 803)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 7.500 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 66.840 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.180 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20896 Z= 0.271 Angle : 0.722 9.208 28328 Z= 0.413 Chirality : 0.350 5.098 3040 Planarity : 0.004 0.055 3612 Dihedral : 19.553 147.861 7832 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 0.75 % Favored : 98.13 % 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: -0.01 (0.18), residues: 2476 helix: 1.34 (0.15), residues: 1232 sheet: -1.32 (0.29), residues: 300 loop : -1.36 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 106 HIS 0.004 0.001 HIS B 178 PHE 0.013 0.001 PHE B 103 TYR 0.019 0.001 TYR G 348 ARG 0.003 0.000 ARG F 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 2.380 Fit side-chains REVERT: A 102 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: B 102 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4402 (m-10) REVERT: B 419 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5423 (mtt) REVERT: C 102 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.4707 (m-80) REVERT: D 102 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4578 (m-80) outliers start: 24 outliers final: 2 residues processed: 276 average time/residue: 1.0483 time to fit residues: 336.9576 Evaluate side-chains 192 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 102 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 9.9990 chunk 187 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 223 ASN C 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20896 Z= 0.194 Angle : 0.566 7.927 28328 Z= 0.276 Chirality : 0.042 0.185 3040 Planarity : 0.004 0.048 3612 Dihedral : 7.641 100.323 3082 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.35 % Allowed : 10.21 % Favored : 88.43 % 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: -0.00 (0.18), residues: 2476 helix: 1.28 (0.15), residues: 1240 sheet: -1.08 (0.30), residues: 296 loop : -1.37 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 106 HIS 0.003 0.001 HIS C 478 PHE 0.016 0.001 PHE A 433 TYR 0.023 0.002 TYR B 44 ARG 0.009 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 2.060 Fit side-chains outliers start: 29 outliers final: 6 residues processed: 206 average time/residue: 1.0906 time to fit residues: 261.5509 Evaluate side-chains 179 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 450 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 243 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 223 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20896 Z= 0.178 Angle : 0.534 7.820 28328 Z= 0.263 Chirality : 0.040 0.165 3040 Planarity : 0.003 0.046 3612 Dihedral : 6.393 96.374 3071 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.54 % Allowed : 12.59 % Favored : 85.87 % 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: 0.10 (0.18), residues: 2476 helix: 1.43 (0.15), residues: 1232 sheet: -1.10 (0.31), residues: 272 loop : -1.35 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 182 HIS 0.003 0.001 HIS C 205 PHE 0.009 0.001 PHE C 179 TYR 0.023 0.001 TYR C 600 ARG 0.010 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: A 182 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.7109 (p90) REVERT: A 387 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7670 (pttt) outliers start: 33 outliers final: 11 residues processed: 202 average time/residue: 1.0609 time to fit residues: 251.0710 Evaluate side-chains 178 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 469 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 0.5980 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20896 Z= 0.167 Angle : 0.522 9.863 28328 Z= 0.257 Chirality : 0.039 0.164 3040 Planarity : 0.003 0.047 3612 Dihedral : 5.676 87.917 3069 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.77 % Allowed : 14.69 % Favored : 83.54 % 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: 0.17 (0.18), residues: 2476 helix: 1.53 (0.15), residues: 1204 sheet: -1.02 (0.30), residues: 296 loop : -1.34 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 182 HIS 0.003 0.000 HIS B 205 PHE 0.009 0.001 PHE A 220 TYR 0.023 0.001 TYR D 600 ARG 0.011 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: A 182 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7267 (p90) outliers start: 38 outliers final: 21 residues processed: 198 average time/residue: 0.9711 time to fit residues: 227.9543 Evaluate side-chains 194 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 165 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN D 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20896 Z= 0.278 Angle : 0.587 9.289 28328 Z= 0.294 Chirality : 0.042 0.170 3040 Planarity : 0.004 0.053 3612 Dihedral : 5.915 89.354 3069 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.61 % Allowed : 14.93 % Favored : 82.46 % 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: -0.05 (0.17), residues: 2476 helix: 1.31 (0.15), residues: 1200 sheet: -1.08 (0.33), residues: 248 loop : -1.39 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 106 HIS 0.003 0.001 HIS C 478 PHE 0.016 0.001 PHE B 307 TYR 0.025 0.002 TYR B 600 ARG 0.010 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 180 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6594 (t) cc_final: 0.6325 (m) REVERT: A 182 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.7271 (p90) REVERT: A 514 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: C 368 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mtp) REVERT: D 115 VAL cc_start: 0.6758 (t) cc_final: 0.6489 (m) REVERT: D 182 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.7173 (p90) REVERT: D 205 HIS cc_start: 0.7541 (m-70) cc_final: 0.7294 (m170) REVERT: D 514 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7588 (m-80) outliers start: 56 outliers final: 28 residues processed: 210 average time/residue: 0.9832 time to fit residues: 244.9866 Evaluate side-chains 206 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 0.2980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20896 Z= 0.165 Angle : 0.535 10.131 28328 Z= 0.263 Chirality : 0.039 0.139 3040 Planarity : 0.003 0.041 3612 Dihedral : 5.516 89.625 3068 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.96 % Allowed : 16.23 % Favored : 81.81 % 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: 0.09 (0.17), residues: 2476 helix: 1.49 (0.15), residues: 1200 sheet: -1.43 (0.33), residues: 228 loop : -1.30 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 106 HIS 0.003 0.001 HIS C 205 PHE 0.013 0.001 PHE C 220 TYR 0.024 0.001 TYR C 600 ARG 0.010 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6588 (t) cc_final: 0.6313 (m) REVERT: A 182 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.7305 (p90) REVERT: B 514 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: C 368 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: C 387 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7734 (pttt) REVERT: D 115 VAL cc_start: 0.6647 (t) cc_final: 0.6400 (m) REVERT: D 368 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8064 (mtp) outliers start: 42 outliers final: 21 residues processed: 200 average time/residue: 0.9704 time to fit residues: 230.2355 Evaluate side-chains 197 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS B 223 ASN B 226 ASN B 260 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 20896 Z= 0.445 Angle : 0.685 9.809 28328 Z= 0.347 Chirality : 0.047 0.213 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.544 86.560 3068 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.33 % Allowed : 16.32 % Favored : 81.34 % 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: -0.36 (0.17), residues: 2476 helix: 1.05 (0.15), residues: 1220 sheet: -1.53 (0.33), residues: 228 loop : -1.52 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 106 HIS 0.007 0.002 HIS B 478 PHE 0.020 0.002 PHE C 220 TYR 0.027 0.002 TYR B 600 ARG 0.010 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6935 (t) cc_final: 0.6675 (m) REVERT: A 182 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.7278 (p90) REVERT: B 514 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: C 115 VAL cc_start: 0.6837 (t) cc_final: 0.6569 (m) REVERT: C 182 TRP cc_start: 0.7568 (OUTLIER) cc_final: 0.7238 (p90) REVERT: C 416 MET cc_start: 0.5081 (tpp) cc_final: 0.4860 (tpt) REVERT: D 115 VAL cc_start: 0.6947 (t) cc_final: 0.6697 (m) outliers start: 50 outliers final: 24 residues processed: 206 average time/residue: 1.0233 time to fit residues: 249.3536 Evaluate side-chains 193 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 518 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS B 226 ASN B 260 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20896 Z= 0.271 Angle : 0.592 8.650 28328 Z= 0.297 Chirality : 0.042 0.182 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.266 89.391 3068 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.77 % Allowed : 17.16 % Favored : 81.06 % 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: -0.29 (0.17), residues: 2476 helix: 1.14 (0.15), residues: 1224 sheet: -1.60 (0.33), residues: 228 loop : -1.52 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 106 HIS 0.004 0.001 HIS C 478 PHE 0.014 0.001 PHE C 179 TYR 0.025 0.001 TYR C 600 ARG 0.007 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6784 (t) cc_final: 0.6525 (m) REVERT: A 182 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.7338 (p90) REVERT: A 427 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7602 (ptt) REVERT: A 514 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: E 333 MET cc_start: 0.5718 (mmp) cc_final: 0.5396 (mmm) REVERT: B 114 VAL cc_start: 0.7199 (m) cc_final: 0.6864 (m) REVERT: B 244 MET cc_start: 0.6048 (ppp) cc_final: 0.5792 (ppp) REVERT: D 115 VAL cc_start: 0.6801 (t) cc_final: 0.6572 (m) REVERT: D 514 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7488 (m-80) outliers start: 38 outliers final: 22 residues processed: 197 average time/residue: 1.0044 time to fit residues: 233.0066 Evaluate side-chains 188 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.2980 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20896 Z= 0.227 Angle : 0.571 10.935 28328 Z= 0.285 Chirality : 0.041 0.166 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.094 89.512 3068 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 17.86 % Favored : 80.74 % 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: -0.24 (0.17), residues: 2476 helix: 1.21 (0.15), residues: 1228 sheet: -1.68 (0.32), residues: 228 loop : -1.50 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 106 HIS 0.003 0.001 HIS D 478 PHE 0.014 0.001 PHE B 179 TYR 0.025 0.002 TYR A 600 ARG 0.007 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 2.332 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7469 (ptt) REVERT: A 514 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: B 114 VAL cc_start: 0.7124 (m) cc_final: 0.6794 (m) REVERT: D 514 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7455 (m-80) outliers start: 30 outliers final: 21 residues processed: 185 average time/residue: 1.0218 time to fit residues: 225.6812 Evaluate side-chains 179 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 227 optimal weight: 0.0870 chunk 196 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20896 Z= 0.179 Angle : 0.563 11.698 28328 Z= 0.278 Chirality : 0.040 0.180 3040 Planarity : 0.003 0.040 3612 Dihedral : 5.929 89.756 3068 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.45 % Allowed : 18.14 % Favored : 80.41 % 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: -0.11 (0.17), residues: 2476 helix: 1.34 (0.15), residues: 1228 sheet: -1.68 (0.32), residues: 228 loop : -1.45 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 106 HIS 0.003 0.001 HIS B 268 PHE 0.014 0.001 PHE B 227 TYR 0.025 0.001 TYR C 600 ARG 0.007 0.000 ARG C 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 2.086 Fit side-chains REVERT: A 427 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7487 (ptt) REVERT: E 333 MET cc_start: 0.5714 (mmp) cc_final: 0.5351 (mmm) REVERT: B 114 VAL cc_start: 0.7149 (m) cc_final: 0.6808 (m) outliers start: 31 outliers final: 21 residues processed: 181 average time/residue: 0.9359 time to fit residues: 199.5236 Evaluate side-chains 176 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.200565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159234 restraints weight = 45920.718| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.58 r_work: 0.3521 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20896 Z= 0.217 Angle : 0.579 11.863 28328 Z= 0.286 Chirality : 0.041 0.212 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.002 89.006 3068 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.31 % Allowed : 18.24 % Favored : 80.46 % 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: -0.13 (0.17), residues: 2476 helix: 1.30 (0.15), residues: 1228 sheet: -1.67 (0.32), residues: 228 loop : -1.43 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 106 HIS 0.003 0.001 HIS C 478 PHE 0.013 0.001 PHE B 227 TYR 0.025 0.001 TYR C 600 ARG 0.006 0.000 ARG C 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.51 seconds wall clock time: 96 minutes 24.62 seconds (5784.62 seconds total)