Starting phenix.real_space_refine on Sun Mar 17 10:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/03_2024/6ka4_9954.pdb" } resolution = 3.4 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= 0.004 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 108 5.16 5 C 11244 2.51 5 N 2960 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D GLU 519": "OE1" <-> "OE2" Residue "D GLU 538": "OE1" <-> "OE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D GLU 553": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 538": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C GLU 550": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4375 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4375 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4375 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4375 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.19, per 1000 atoms: 0.53 Number of scatterers: 17500 At special positions: 0 Unit cell: (129.347, 121.508, 105.83, 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 108 16.00 O 3188 8.00 N 2960 7.00 C 11244 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: 7.09 Conformation dependent library (CDL) restraints added in 3.3 seconds 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 66.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 27 through 53 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 131 Proline residue: A 119 - end of helix removed outlier: 3.700A pdb=" N VAL A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 180 removed outlier: 4.049A pdb=" N GLU A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 200 removed outlier: 3.731A pdb=" N GLN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.517A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 434 through 448 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.960A pdb=" N LEU A 457 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.297A pdb=" N LEU A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 521 Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 removed outlier: 3.560A pdb=" N THR A 552 " --> pdb=" O TRP A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'D' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 24 Processing helix chain 'D' and resid 27 through 53 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 88 Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 131 Proline residue: D 119 - end of helix removed outlier: 3.701A pdb=" N VAL D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.049A pdb=" N GLU D 179 " --> pdb=" O CYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 200 removed outlier: 3.730A pdb=" N GLN D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.516A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.591A pdb=" N LYS D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 318 " --> pdb=" O MET D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 350 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 434 through 448 Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.961A pdb=" N LEU D 457 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU D 485 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 486 " --> pdb=" O ILE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 517 removed outlier: 3.921A pdb=" N ARG D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 509 " --> pdb=" O ARG D 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 521 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN D 545 " --> pdb=" O THR D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 552 removed outlier: 3.561A pdb=" N THR D 552 " --> pdb=" O TRP D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 552' Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 559 through 574 Processing helix chain 'B' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 27 through 53 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 109 through 131 Proline residue: B 119 - end of helix removed outlier: 3.700A pdb=" N VAL B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 150 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU B 169 " --> pdb=" O ARG B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 171 through 180 removed outlier: 4.050A pdb=" N GLU B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 200 removed outlier: 3.730A pdb=" N GLN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.517A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 434 through 448 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.961A pdb=" N LEU B 457 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.739A pdb=" N ARG B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU B 485 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 521 Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 552 removed outlier: 3.561A pdb=" N THR B 552 " --> pdb=" O TRP B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 27 through 53 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 88 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 131 Proline residue: C 119 - end of helix removed outlier: 3.701A pdb=" N VAL C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU C 169 " --> pdb=" O ARG C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 171 through 180 removed outlier: 4.050A pdb=" N GLU C 179 " --> pdb=" O CYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 200 removed outlier: 3.731A pdb=" N GLN C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.634A pdb=" N ASP C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 Proline residue: C 273 - end of helix Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.518A pdb=" N LEU C 281 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 318 " --> pdb=" O MET C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 350 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 434 through 448 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.960A pdb=" N LEU C 457 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU C 485 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 486 " --> pdb=" O ILE C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 509 " --> pdb=" O ARG C 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 521 Processing helix chain 'C' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN C 545 " --> pdb=" O THR C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 552 removed outlier: 3.560A pdb=" N THR C 552 " --> pdb=" O TRP C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR A 289 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU A 306 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 291 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 251 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AA3, first strand: chain 'D' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR D 289 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU D 306 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS D 291 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 251 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 362 through 366 Processing sheet with id=AA5, first strand: chain 'B' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR B 289 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 306 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS B 291 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 251 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366 Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR C 289 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU C 306 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 291 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 251 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 362 through 366 936 hydrogen bonds defined for protein. 2700 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: 5.40 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5532 1.34 - 1.46: 2939 1.46 - 1.57: 9257 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 17900 Sorted by residual: bond pdb=" CA VAL D 560 " pdb=" CB VAL D 560 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.74e+00 bond pdb=" CA SER D 222 " pdb=" C SER D 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.66e+00 bond pdb=" CA SER A 222 " pdb=" C SER A 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.62e+00 bond pdb=" CA SER B 222 " pdb=" C SER B 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.62e+00 bond pdb=" CA SER C 222 " pdb=" C SER C 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.60e+00 ... (remaining 17895 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.72: 352 105.72 - 112.81: 9539 112.81 - 119.89: 6241 119.89 - 126.98: 7729 126.98 - 134.07: 251 Bond angle restraints: 24112 Sorted by residual: angle pdb=" N GLN D 3 " pdb=" CA GLN D 3 " pdb=" C GLN D 3 " ideal model delta sigma weight residual 113.43 106.18 7.25 1.26e+00 6.30e-01 3.31e+01 angle pdb=" N GLN A 3 " pdb=" CA GLN A 3 " pdb=" C GLN A 3 " ideal model delta sigma weight residual 113.43 106.19 7.24 1.26e+00 6.30e-01 3.30e+01 angle pdb=" N GLN C 3 " pdb=" CA GLN C 3 " pdb=" C GLN C 3 " ideal model delta sigma weight residual 113.43 106.21 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N GLN B 3 " pdb=" CA GLN B 3 " pdb=" C GLN B 3 " ideal model delta sigma weight residual 113.43 106.21 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N SER C 222 " pdb=" CA SER C 222 " pdb=" C SER C 222 " ideal model delta sigma weight residual 113.16 120.90 -7.74 1.42e+00 4.96e-01 2.97e+01 ... (remaining 24107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 9480 15.41 - 30.82: 1059 30.82 - 46.23: 237 46.23 - 61.64: 32 61.64 - 77.05: 24 Dihedral angle restraints: 10832 sinusoidal: 4568 harmonic: 6264 Sorted by residual: dihedral pdb=" CA THR B 253 " pdb=" C THR B 253 " pdb=" N TRP B 254 " pdb=" CA TRP B 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR A 253 " pdb=" C THR A 253 " pdb=" N TRP A 254 " pdb=" CA TRP A 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR D 253 " pdb=" C THR D 253 " pdb=" N TRP D 254 " pdb=" CA TRP D 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2068 0.057 - 0.114: 502 0.114 - 0.171: 34 0.171 - 0.229: 4 0.229 - 0.286: 4 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA SER D 222 " pdb=" N SER D 222 " pdb=" C SER D 222 " pdb=" CB SER D 222 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER A 222 " pdb=" N SER A 222 " pdb=" C SER A 222 " pdb=" CB SER A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA SER C 222 " pdb=" N SER C 222 " pdb=" C SER C 222 " pdb=" CB SER C 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2609 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 221 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C GLU B 221 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 221 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 222 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 221 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU A 221 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU A 221 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 222 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 221 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C GLU C 221 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU C 221 " 0.026 2.00e-02 2.50e+03 pdb=" N SER C 222 " 0.023 2.00e-02 2.50e+03 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 236 2.64 - 3.21: 16805 3.21 - 3.77: 26724 3.77 - 4.34: 38005 4.34 - 4.90: 61814 Nonbonded interactions: 143584 Sorted by model distance: nonbonded pdb=" N GLU A 356 " pdb=" OE1 GLU A 356 " model vdw 2.076 2.520 nonbonded pdb=" N GLU B 356 " pdb=" OE1 GLU B 356 " model vdw 2.076 2.520 nonbonded pdb=" N GLU C 356 " pdb=" OE1 GLU C 356 " model vdw 2.076 2.520 nonbonded pdb=" N GLU D 356 " pdb=" OE1 GLU D 356 " model vdw 2.077 2.520 nonbonded pdb=" NZ LYS B 310 " pdb=" OE1 GLU B 318 " model vdw 2.206 2.520 ... (remaining 143579 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 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.720 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 47.780 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.006 0.047 17900 Z= 0.417 Angle : 0.816 7.738 24112 Z= 0.499 Chirality : 0.048 0.286 2612 Planarity : 0.005 0.087 3032 Dihedral : 13.681 77.052 6752 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 2088 helix: 0.41 (0.15), residues: 1212 sheet: 0.11 (0.50), residues: 104 loop : -0.70 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 254 HIS 0.005 0.001 HIS A 204 PHE 0.015 0.002 PHE B 438 TYR 0.012 0.002 TYR B 521 ARG 0.007 0.001 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.201 Fit side-chains REVERT: A 233 ASN cc_start: 0.7955 (m110) cc_final: 0.7691 (m-40) REVERT: A 410 TYR cc_start: 0.7909 (m-80) cc_final: 0.7194 (m-80) REVERT: A 440 MET cc_start: 0.8892 (mmm) cc_final: 0.8132 (tpt) REVERT: D 410 TYR cc_start: 0.7906 (m-80) cc_final: 0.7176 (m-80) REVERT: D 440 MET cc_start: 0.8865 (mmm) cc_final: 0.8135 (tpt) REVERT: D 530 ILE cc_start: 0.6225 (mp) cc_final: 0.5818 (tp) REVERT: B 233 ASN cc_start: 0.7798 (m110) cc_final: 0.7560 (m-40) REVERT: B 410 TYR cc_start: 0.7892 (m-80) cc_final: 0.7150 (m-80) REVERT: B 440 MET cc_start: 0.8883 (mmm) cc_final: 0.8129 (tpt) REVERT: C 410 TYR cc_start: 0.7740 (m-80) cc_final: 0.7028 (m-80) REVERT: C 440 MET cc_start: 0.8850 (mmm) cc_final: 0.8405 (tpt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3222 time to fit residues: 117.9523 Evaluate side-chains 207 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN D 233 ASN B 233 ASN C 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17900 Z= 0.204 Angle : 0.591 9.158 24112 Z= 0.307 Chirality : 0.042 0.143 2612 Planarity : 0.004 0.059 3032 Dihedral : 4.780 18.478 2300 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.82 % Allowed : 7.36 % Favored : 91.82 % 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: 0.40 (0.18), residues: 2088 helix: 0.82 (0.15), residues: 1260 sheet: -0.30 (0.44), residues: 104 loop : -0.47 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 254 HIS 0.004 0.001 HIS D 204 PHE 0.010 0.002 PHE C 476 TYR 0.014 0.001 TYR B 521 ARG 0.002 0.000 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 266 time to evaluate : 2.107 Fit side-chains REVERT: A 138 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 238 GLN cc_start: 0.7063 (tm130) cc_final: 0.6731 (tm-30) REVERT: A 410 TYR cc_start: 0.7717 (m-80) cc_final: 0.7139 (m-80) REVERT: A 440 MET cc_start: 0.8442 (mmm) cc_final: 0.8180 (mmm) REVERT: D 238 GLN cc_start: 0.7010 (tm130) cc_final: 0.6719 (tm-30) REVERT: D 410 TYR cc_start: 0.7741 (m-80) cc_final: 0.7183 (m-80) REVERT: D 440 MET cc_start: 0.8446 (mmm) cc_final: 0.8143 (mmm) REVERT: B 238 GLN cc_start: 0.7121 (tm130) cc_final: 0.6776 (tm-30) REVERT: B 410 TYR cc_start: 0.7727 (m-80) cc_final: 0.7172 (m-80) REVERT: B 440 MET cc_start: 0.8443 (mmm) cc_final: 0.8174 (mmm) REVERT: C 238 GLN cc_start: 0.7129 (tm130) cc_final: 0.6774 (tm-30) REVERT: C 410 TYR cc_start: 0.7802 (m-80) cc_final: 0.7291 (m-80) REVERT: C 440 MET cc_start: 0.8479 (mmm) cc_final: 0.8277 (mmm) outliers start: 16 outliers final: 9 residues processed: 271 average time/residue: 0.3127 time to fit residues: 124.4602 Evaluate side-chains 225 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17900 Z= 0.194 Angle : 0.540 8.678 24112 Z= 0.277 Chirality : 0.040 0.134 2612 Planarity : 0.004 0.049 3032 Dihedral : 4.503 16.706 2300 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.28 % Allowed : 11.76 % Favored : 86.96 % 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: 0.67 (0.18), residues: 2088 helix: 1.05 (0.15), residues: 1284 sheet: -0.87 (0.42), residues: 128 loop : -0.30 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.007 0.001 HIS B 263 PHE 0.009 0.001 PHE C 407 TYR 0.018 0.001 TYR A 509 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 2.054 Fit side-chains REVERT: A 238 GLN cc_start: 0.6886 (tm130) cc_final: 0.6441 (tm-30) REVERT: A 410 TYR cc_start: 0.7639 (m-80) cc_final: 0.7144 (m-80) REVERT: A 440 MET cc_start: 0.8427 (mmm) cc_final: 0.8201 (mmm) REVERT: D 138 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 238 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6455 (tm-30) REVERT: D 410 TYR cc_start: 0.7682 (m-80) cc_final: 0.7209 (m-80) REVERT: B 238 GLN cc_start: 0.6903 (tm130) cc_final: 0.6480 (tm-30) REVERT: B 410 TYR cc_start: 0.7622 (m-80) cc_final: 0.7161 (m-80) REVERT: C 238 GLN cc_start: 0.6938 (tm130) cc_final: 0.6527 (tm-30) REVERT: C 410 TYR cc_start: 0.7708 (m-80) cc_final: 0.7223 (m-80) REVERT: C 530 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6679 (mp) outliers start: 25 outliers final: 16 residues processed: 238 average time/residue: 0.2959 time to fit residues: 106.7679 Evaluate side-chains 226 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 0.0670 chunk 204 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17900 Z= 0.149 Angle : 0.511 7.137 24112 Z= 0.258 Chirality : 0.038 0.127 2612 Planarity : 0.004 0.043 3032 Dihedral : 4.227 16.283 2300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.07 % Allowed : 12.73 % Favored : 86.20 % 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: 0.93 (0.19), residues: 2088 helix: 1.31 (0.15), residues: 1264 sheet: -0.85 (0.41), residues: 128 loop : -0.25 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 254 HIS 0.004 0.001 HIS D 263 PHE 0.010 0.001 PHE C 407 TYR 0.010 0.001 TYR C 521 ARG 0.001 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 2.151 Fit side-chains REVERT: A 138 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7288 (mm-30) REVERT: A 238 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6398 (tm-30) REVERT: A 251 GLU cc_start: 0.7097 (mp0) cc_final: 0.6821 (mt-10) REVERT: A 410 TYR cc_start: 0.7667 (m-80) cc_final: 0.7135 (m-80) REVERT: A 440 MET cc_start: 0.8366 (mmm) cc_final: 0.8151 (mmm) REVERT: D 138 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7209 (mm-30) REVERT: D 195 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 238 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6394 (tm-30) REVERT: D 251 GLU cc_start: 0.7153 (mp0) cc_final: 0.6865 (mt-10) REVERT: D 410 TYR cc_start: 0.7727 (m-80) cc_final: 0.7227 (m-80) REVERT: D 440 MET cc_start: 0.8473 (mmm) cc_final: 0.7842 (mmm) REVERT: B 195 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 238 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6398 (tm-30) REVERT: B 251 GLU cc_start: 0.6967 (mp0) cc_final: 0.6652 (mt-10) REVERT: B 410 TYR cc_start: 0.7656 (m-80) cc_final: 0.7170 (m-80) REVERT: B 440 MET cc_start: 0.8458 (mmm) cc_final: 0.7881 (mmm) REVERT: C 195 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7678 (tm-30) REVERT: C 238 GLN cc_start: 0.6910 (tm-30) cc_final: 0.6442 (tm-30) REVERT: C 410 TYR cc_start: 0.7737 (m-80) cc_final: 0.7198 (m-80) REVERT: C 440 MET cc_start: 0.8482 (mmm) cc_final: 0.7896 (mmm) REVERT: C 530 ILE cc_start: 0.6879 (mp) cc_final: 0.6486 (mp) outliers start: 21 outliers final: 17 residues processed: 238 average time/residue: 0.2834 time to fit residues: 104.3067 Evaluate side-chains 237 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 0.0050 chunk 183 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17900 Z= 0.142 Angle : 0.484 5.988 24112 Z= 0.245 Chirality : 0.038 0.126 2612 Planarity : 0.003 0.040 3032 Dihedral : 4.015 15.939 2300 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.64 % Allowed : 13.55 % Favored : 84.82 % 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: 1.12 (0.19), residues: 2088 helix: 1.49 (0.15), residues: 1264 sheet: -0.76 (0.40), residues: 128 loop : -0.24 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 254 HIS 0.004 0.001 HIS B 204 PHE 0.009 0.001 PHE C 407 TYR 0.010 0.001 TYR C 42 ARG 0.001 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.976 Fit side-chains REVERT: A 138 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 159 MET cc_start: 0.8980 (tpp) cc_final: 0.8395 (tpp) REVERT: A 195 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 238 GLN cc_start: 0.6811 (tm-30) cc_final: 0.6196 (tm-30) REVERT: A 257 GLU cc_start: 0.6263 (tp30) cc_final: 0.6052 (tp30) REVERT: A 410 TYR cc_start: 0.7717 (m-80) cc_final: 0.7184 (m-80) REVERT: D 138 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7203 (mm-30) REVERT: D 159 MET cc_start: 0.9087 (tpp) cc_final: 0.8504 (tpp) REVERT: D 195 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7900 (tm-30) REVERT: D 238 GLN cc_start: 0.6837 (tm-30) cc_final: 0.6253 (tm-30) REVERT: D 257 GLU cc_start: 0.6262 (tp30) cc_final: 0.6041 (tp30) REVERT: D 410 TYR cc_start: 0.7977 (m-80) cc_final: 0.7454 (m-80) REVERT: D 440 MET cc_start: 0.8406 (mmm) cc_final: 0.7372 (mmm) REVERT: B 138 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 159 MET cc_start: 0.8900 (tpp) cc_final: 0.8691 (tpp) REVERT: B 195 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 238 GLN cc_start: 0.6835 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 257 GLU cc_start: 0.6260 (tp30) cc_final: 0.6051 (tp30) REVERT: B 410 TYR cc_start: 0.7691 (m-80) cc_final: 0.7173 (m-80) REVERT: B 440 MET cc_start: 0.8402 (mmm) cc_final: 0.7409 (mmm) REVERT: C 195 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 238 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6257 (tm-30) REVERT: C 257 GLU cc_start: 0.6187 (tp30) cc_final: 0.5983 (tp30) REVERT: C 410 TYR cc_start: 0.7728 (m-80) cc_final: 0.7146 (m-80) REVERT: C 440 MET cc_start: 0.8413 (mmm) cc_final: 0.7419 (mmm) outliers start: 32 outliers final: 25 residues processed: 234 average time/residue: 0.3074 time to fit residues: 109.8541 Evaluate side-chains 228 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.0570 chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17900 Z= 0.157 Angle : 0.498 8.111 24112 Z= 0.247 Chirality : 0.038 0.130 2612 Planarity : 0.003 0.037 3032 Dihedral : 3.959 15.671 2300 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.04 % Allowed : 13.70 % Favored : 84.25 % 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: 1.21 (0.19), residues: 2088 helix: 1.58 (0.15), residues: 1264 sheet: -0.64 (0.39), residues: 128 loop : -0.24 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 254 HIS 0.003 0.001 HIS C 204 PHE 0.010 0.001 PHE A 4 TYR 0.010 0.001 TYR B 42 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 2.222 Fit side-chains REVERT: A 138 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 195 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 238 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6249 (tm-30) REVERT: A 251 GLU cc_start: 0.6999 (mp0) cc_final: 0.6650 (mt-10) REVERT: A 257 GLU cc_start: 0.6177 (tp30) cc_final: 0.5972 (tp30) REVERT: A 410 TYR cc_start: 0.7933 (m-80) cc_final: 0.7395 (m-80) REVERT: D 138 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 159 MET cc_start: 0.9002 (tpp) cc_final: 0.8474 (mmm) REVERT: D 195 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 238 GLN cc_start: 0.6900 (tm-30) cc_final: 0.6290 (tm-30) REVERT: D 257 GLU cc_start: 0.6276 (tp30) cc_final: 0.6051 (tp30) REVERT: D 410 TYR cc_start: 0.7886 (m-80) cc_final: 0.7319 (m-80) REVERT: D 440 MET cc_start: 0.8547 (mmm) cc_final: 0.7423 (mmm) REVERT: B 138 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7140 (mm-30) REVERT: B 195 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 238 GLN cc_start: 0.6865 (tm-30) cc_final: 0.6222 (tm-30) REVERT: B 410 TYR cc_start: 0.7937 (m-80) cc_final: 0.7400 (m-80) REVERT: B 440 MET cc_start: 0.8570 (mmm) cc_final: 0.7421 (mmm) REVERT: C 138 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7110 (mm-30) REVERT: C 195 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 238 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6328 (tm-30) REVERT: C 410 TYR cc_start: 0.7962 (m-80) cc_final: 0.7397 (m-80) REVERT: C 440 MET cc_start: 0.8688 (mmm) cc_final: 0.7557 (mmm) outliers start: 40 outliers final: 34 residues processed: 233 average time/residue: 0.2857 time to fit residues: 102.5709 Evaluate side-chains 244 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17900 Z= 0.359 Angle : 0.602 7.756 24112 Z= 0.300 Chirality : 0.043 0.148 2612 Planarity : 0.004 0.038 3032 Dihedral : 4.286 16.399 2300 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.81 % Allowed : 14.01 % Favored : 83.18 % 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: 1.04 (0.18), residues: 2088 helix: 1.48 (0.15), residues: 1228 sheet: -0.30 (0.41), residues: 128 loop : -0.40 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 254 HIS 0.004 0.001 HIS A 204 PHE 0.015 0.002 PHE C 4 TYR 0.012 0.002 TYR B 521 ARG 0.005 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 2.274 Fit side-chains REVERT: A 123 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 238 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6415 (tm-30) REVERT: A 251 GLU cc_start: 0.7064 (mp0) cc_final: 0.6717 (mt-10) REVERT: A 410 TYR cc_start: 0.7932 (m-80) cc_final: 0.7429 (m-80) REVERT: A 440 MET cc_start: 0.8456 (mmm) cc_final: 0.8200 (mmm) REVERT: D 123 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 138 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7245 (mm-30) REVERT: D 195 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7871 (tm-30) REVERT: D 238 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6045 (tm-30) REVERT: D 251 GLU cc_start: 0.7049 (mp0) cc_final: 0.6682 (mt-10) REVERT: D 410 TYR cc_start: 0.7933 (m-80) cc_final: 0.7380 (m-80) REVERT: B 123 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 238 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6423 (tm-30) REVERT: B 251 GLU cc_start: 0.7227 (mp0) cc_final: 0.6808 (mt-10) REVERT: B 410 TYR cc_start: 0.7924 (m-80) cc_final: 0.7415 (m-80) REVERT: C 238 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6462 (tm-30) REVERT: C 410 TYR cc_start: 0.7938 (m-80) cc_final: 0.7314 (m-80) outliers start: 55 outliers final: 42 residues processed: 225 average time/residue: 0.2833 time to fit residues: 98.4635 Evaluate side-chains 226 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17900 Z= 0.169 Angle : 0.515 7.692 24112 Z= 0.257 Chirality : 0.039 0.133 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.106 15.574 2300 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 15.13 % 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: 1.14 (0.18), residues: 2088 helix: 1.56 (0.15), residues: 1240 sheet: -0.45 (0.38), residues: 128 loop : -0.34 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 254 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE D 4 TYR 0.013 0.001 TYR C 42 ARG 0.002 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 2.367 Fit side-chains REVERT: A 195 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 238 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6301 (tm-30) REVERT: A 251 GLU cc_start: 0.7020 (mp0) cc_final: 0.6712 (mt-10) REVERT: A 344 MET cc_start: 0.8983 (mmm) cc_final: 0.8739 (mmp) REVERT: A 410 TYR cc_start: 0.8025 (m-80) cc_final: 0.7410 (m-80) REVERT: A 440 MET cc_start: 0.8453 (mmm) cc_final: 0.8177 (mmm) REVERT: D 138 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7155 (mm-30) REVERT: D 195 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7957 (tm-30) REVERT: D 238 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6382 (tm-30) REVERT: D 251 GLU cc_start: 0.6977 (mp0) cc_final: 0.6680 (mt-10) REVERT: D 410 TYR cc_start: 0.7942 (m-80) cc_final: 0.7318 (m-80) REVERT: D 440 MET cc_start: 0.8569 (mmm) cc_final: 0.8067 (mmm) REVERT: B 138 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 195 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 238 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6316 (tm-30) REVERT: B 251 GLU cc_start: 0.7140 (mp0) cc_final: 0.6754 (mt-10) REVERT: B 344 MET cc_start: 0.8982 (mmm) cc_final: 0.8739 (mmp) REVERT: B 410 TYR cc_start: 0.7921 (m-80) cc_final: 0.7331 (m-80) REVERT: B 440 MET cc_start: 0.8566 (mmm) cc_final: 0.8087 (mmm) REVERT: C 195 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 238 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 410 TYR cc_start: 0.7919 (m-80) cc_final: 0.7301 (m-80) REVERT: C 440 MET cc_start: 0.8565 (mmm) cc_final: 0.8090 (mmm) outliers start: 47 outliers final: 40 residues processed: 235 average time/residue: 0.2804 time to fit residues: 102.2184 Evaluate side-chains 238 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17900 Z= 0.172 Angle : 0.520 10.992 24112 Z= 0.255 Chirality : 0.039 0.131 2612 Planarity : 0.003 0.034 3032 Dihedral : 4.022 15.411 2300 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.30 % Allowed : 15.80 % Favored : 81.90 % 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: 1.08 (0.18), residues: 2088 helix: 1.49 (0.15), residues: 1264 sheet: -1.31 (0.42), residues: 80 loop : -0.30 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 254 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE C 4 TYR 0.013 0.001 TYR D 509 ARG 0.002 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 2.163 Fit side-chains REVERT: A 195 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 238 GLN cc_start: 0.6995 (tm-30) cc_final: 0.6256 (tm-30) REVERT: A 251 GLU cc_start: 0.7014 (mp0) cc_final: 0.6745 (mt-10) REVERT: A 344 MET cc_start: 0.8989 (mmm) cc_final: 0.8757 (mmp) REVERT: A 410 TYR cc_start: 0.7789 (m-80) cc_final: 0.7126 (m-80) REVERT: A 440 MET cc_start: 0.8339 (mmm) cc_final: 0.8065 (mmm) REVERT: D 238 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6318 (tm-30) REVERT: D 251 GLU cc_start: 0.6968 (mp0) cc_final: 0.6703 (mt-10) REVERT: D 410 TYR cc_start: 0.7941 (m-80) cc_final: 0.7265 (m-80) REVERT: D 440 MET cc_start: 0.8543 (mmm) cc_final: 0.8008 (mmm) REVERT: B 195 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 238 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6267 (tm-30) REVERT: B 251 GLU cc_start: 0.7135 (mp0) cc_final: 0.6760 (mt-10) REVERT: B 344 MET cc_start: 0.8995 (mmm) cc_final: 0.8758 (mmp) REVERT: B 410 TYR cc_start: 0.7931 (m-80) cc_final: 0.7322 (m-80) REVERT: B 440 MET cc_start: 0.8546 (mmm) cc_final: 0.7760 (mmm) REVERT: C 195 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7917 (tm-30) REVERT: C 238 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6370 (tm-30) REVERT: C 410 TYR cc_start: 0.7934 (m-80) cc_final: 0.7308 (m-80) REVERT: C 440 MET cc_start: 0.8545 (mmm) cc_final: 0.8023 (mmm) outliers start: 45 outliers final: 39 residues processed: 223 average time/residue: 0.2739 time to fit residues: 94.6209 Evaluate side-chains 231 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 211 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17900 Z= 0.183 Angle : 0.546 11.360 24112 Z= 0.263 Chirality : 0.039 0.132 2612 Planarity : 0.003 0.034 3032 Dihedral : 4.033 15.407 2300 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.99 % Allowed : 16.36 % Favored : 81.65 % 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: 1.09 (0.18), residues: 2088 helix: 1.51 (0.15), residues: 1264 sheet: -1.28 (0.42), residues: 80 loop : -0.33 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 254 HIS 0.003 0.001 HIS B 204 PHE 0.011 0.001 PHE C 4 TYR 0.014 0.001 TYR C 42 ARG 0.002 0.000 ARG A 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 2.213 Fit side-chains REVERT: A 195 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 238 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6246 (tm-30) REVERT: A 251 GLU cc_start: 0.6963 (mp0) cc_final: 0.6678 (mt-10) REVERT: A 344 MET cc_start: 0.8997 (mmm) cc_final: 0.8765 (mmp) REVERT: A 410 TYR cc_start: 0.7807 (m-80) cc_final: 0.7183 (m-80) REVERT: A 440 MET cc_start: 0.8297 (mmm) cc_final: 0.8011 (mmm) REVERT: D 238 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6314 (tm-30) REVERT: D 251 GLU cc_start: 0.6995 (mp0) cc_final: 0.6736 (mt-10) REVERT: D 410 TYR cc_start: 0.7822 (m-80) cc_final: 0.7075 (m-80) REVERT: B 195 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 238 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6269 (tm-30) REVERT: B 251 GLU cc_start: 0.6978 (mp0) cc_final: 0.6762 (mt-10) REVERT: B 329 SER cc_start: 0.8918 (t) cc_final: 0.8713 (t) REVERT: B 344 MET cc_start: 0.8997 (mmm) cc_final: 0.8769 (mmp) REVERT: B 410 TYR cc_start: 0.7808 (m-80) cc_final: 0.7134 (m-80) REVERT: C 195 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 238 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6365 (tm-30) REVERT: C 410 TYR cc_start: 0.7942 (m-80) cc_final: 0.7184 (m-80) outliers start: 39 outliers final: 37 residues processed: 222 average time/residue: 0.2838 time to fit residues: 97.3117 Evaluate side-chains 231 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 263 HIS D 27 ASN D 263 HIS B 263 HIS C 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115224 restraints weight = 24629.772| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.26 r_work: 0.3206 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17900 Z= 0.147 Angle : 0.531 10.948 24112 Z= 0.255 Chirality : 0.038 0.129 2612 Planarity : 0.003 0.034 3032 Dihedral : 3.942 15.192 2300 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.69 % Allowed : 16.77 % Favored : 81.54 % 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: 1.18 (0.18), residues: 2088 helix: 1.59 (0.15), residues: 1264 sheet: -1.18 (0.42), residues: 80 loop : -0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 254 HIS 0.003 0.001 HIS D 204 PHE 0.010 0.001 PHE C 438 TYR 0.013 0.001 TYR C 42 ARG 0.002 0.000 ARG C 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.32 seconds wall clock time: 62 minutes 47.18 seconds (3767.18 seconds total)