Starting phenix.real_space_refine (version: dev) on Tue Dec 13 22:16:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/12_2022/6ka4_9954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/12_2022/6ka4_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_9954/12_2022/6ka4_9954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/12_2022/6ka4_9954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/12_2022/6ka4_9954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/12_2022/6ka4_9954.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 9.56, per 1000 atoms: 0.55 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: 6.41 Conformation dependent library (CDL) restraints added in 2.6 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: 0.97 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: 5.49 Time building geometry restraints manager: 7.02 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 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. 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: 0.360 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: 3.270 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.160 Process input model: 44.110 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 52.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 % 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 *********************** 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 : 2.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3232 time to fit residues: 119.2611 Evaluate side-chains 205 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9739 ------------------------------------------------------------------------------- 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: 5.9990 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 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17900 Z= 0.205 Angle : 0.587 8.740 24112 Z= 0.304 Chirality : 0.042 0.142 2612 Planarity : 0.004 0.058 3032 Dihedral : 4.777 18.360 2300 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.02 % 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: 0.38 (0.18), residues: 2088 helix: 0.81 (0.15), residues: 1260 sheet: -0.33 (0.43), residues: 104 loop : -0.49 (0.23), residues: 724 *********************** 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 292 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 2.233 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 280 average time/residue: 0.3166 time to fit residues: 131.3270 Evaluate side-chains 214 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1588 time to fit residues: 5.4132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 0.0270 chunk 171 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17900 Z= 0.185 Angle : 0.543 8.720 24112 Z= 0.279 Chirality : 0.040 0.132 2612 Planarity : 0.004 0.049 3032 Dihedral : 4.486 16.711 2300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.26 % 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: 0.68 (0.18), residues: 2088 helix: 1.08 (0.15), residues: 1260 sheet: -0.92 (0.42), residues: 128 loop : -0.26 (0.23), residues: 700 *********************** 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 235 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 2.162 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 231 average time/residue: 0.3006 time to fit residues: 105.3237 Evaluate side-chains 205 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1584 time to fit residues: 4.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 17900 Z= 0.352 Angle : 0.609 7.249 24112 Z= 0.310 Chirality : 0.043 0.142 2612 Planarity : 0.004 0.045 3032 Dihedral : 4.544 17.167 2300 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.48 % 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 (0.19), residues: 2088 helix: 1.11 (0.15), residues: 1252 sheet: -0.10 (0.45), residues: 112 loop : -0.54 (0.23), residues: 724 *********************** 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 228 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 2.293 Fit side-chains outliers start: 29 outliers final: 28 residues processed: 216 average time/residue: 0.2810 time to fit residues: 93.5465 Evaluate side-chains 223 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1509 time to fit residues: 11.0796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 17900 Z= 0.162 Angle : 0.511 6.146 24112 Z= 0.263 Chirality : 0.039 0.126 2612 Planarity : 0.004 0.039 3032 Dihedral : 4.263 16.175 2300 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2088 helix: 1.29 (0.15), residues: 1240 sheet: -0.73 (0.42), residues: 128 loop : -0.33 (0.23), residues: 720 *********************** 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 253 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 2.256 Fit side-chains outliers start: 28 outliers final: 6 residues processed: 240 average time/residue: 0.2680 time to fit residues: 100.7663 Evaluate side-chains 204 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1595 time to fit residues: 4.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 94 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 17900 Z= 0.164 Angle : 0.517 6.985 24112 Z= 0.261 Chirality : 0.039 0.131 2612 Planarity : 0.004 0.037 3032 Dihedral : 4.130 15.750 2300 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.46 % 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: 1.00 (0.18), residues: 2088 helix: 1.47 (0.15), residues: 1240 sheet: -0.78 (0.40), residues: 128 loop : -0.39 (0.23), residues: 720 *********************** 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 223 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 2.189 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 219 average time/residue: 0.2751 time to fit residues: 93.8833 Evaluate side-chains 207 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1524 time to fit residues: 4.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.0050 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 0.0060 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 204 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 17900 Z= 0.150 Angle : 0.510 7.754 24112 Z= 0.255 Chirality : 0.038 0.128 2612 Planarity : 0.004 0.037 3032 Dihedral : 4.025 15.403 2300 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.02 % 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: 1.63 (0.15), residues: 1240 sheet: -1.71 (0.41), residues: 80 loop : -0.47 (0.22), residues: 768 *********************** 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 240 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 2.245 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 232 average time/residue: 0.2864 time to fit residues: 103.0492 Evaluate side-chains 208 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1663 time to fit residues: 7.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.0470 chunk 185 optimal weight: 5.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 204 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN B 204 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 17900 Z= 0.183 Angle : 0.538 7.716 24112 Z= 0.265 Chirality : 0.039 0.129 2612 Planarity : 0.004 0.036 3032 Dihedral : 4.026 15.463 2300 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2088 helix: 1.70 (0.15), residues: 1240 sheet: -1.49 (0.41), residues: 80 loop : -0.44 (0.22), residues: 768 *********************** 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 211 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 2.276 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 208 average time/residue: 0.2708 time to fit residues: 87.2300 Evaluate side-chains 198 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1490 time to fit residues: 4.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 190 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 204 HIS A 238 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17900 Z= 0.185 Angle : 0.533 7.866 24112 Z= 0.264 Chirality : 0.039 0.129 2612 Planarity : 0.004 0.036 3032 Dihedral : 4.049 15.428 2300 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.82 % 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: 1.18 (0.18), residues: 2088 helix: 1.70 (0.15), residues: 1240 sheet: -1.29 (0.42), residues: 80 loop : -0.45 (0.21), residues: 768 *********************** 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 208 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.205 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 202 average time/residue: 0.2836 time to fit residues: 87.6273 Evaluate side-chains 197 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1475 time to fit residues: 6.0289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS D 263 HIS B 204 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 17900 Z= 0.152 Angle : 0.527 7.874 24112 Z= 0.259 Chirality : 0.039 0.125 2612 Planarity : 0.003 0.037 3032 Dihedral : 3.974 15.180 2300 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.46 % 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: 1.22 (0.18), residues: 2088 helix: 1.66 (0.15), residues: 1264 sheet: -1.10 (0.42), residues: 80 loop : -0.38 (0.22), residues: 744 ********************** 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 206 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 2.407 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 202 average time/residue: 0.2936 time to fit residues: 92.2140 Evaluate side-chains 190 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1657 time to fit residues: 4.7810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.0980 chunk 51 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 204 HIS B 238 GLN C 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115486 restraints weight = 24638.590| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.24 r_work: 0.3212 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2799 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= 0.156 Angle : 0.522 7.661 24112 Z= 0.259 Chirality : 0.039 0.127 2612 Planarity : 0.004 0.037 3032 Dihedral : 4.010 15.477 2300 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.15 % 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: 1.23 (0.18), residues: 2088 helix: 1.67 (0.15), residues: 1264 sheet: -0.95 (0.43), residues: 80 loop : -0.40 (0.22), residues: 744 =============================================================================== Job complete usr+sys time: 3176.03 seconds wall clock time: 59 minutes 14.35 seconds (3554.35 seconds total)