Starting phenix.real_space_refine (version: dev) on Mon Dec 12 01:04:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/12_2022/7l1k_23110_updated.pdb" } resolution = 3.16 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= 0.001 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1216 atoms to isotropic. 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 GLU 25": "OE1" <-> "OE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7217 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1233 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 5315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 660, 5309 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 628} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 660, 5309 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 628} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 5420 Chain: "C" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 555 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Link IDs: {'PTRANS': 1, 'TRANS': 2} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 190 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 190 " occ=0.50 Time building chain proxies: 7.26, per 1000 atoms: 1.01 Number of scatterers: 7217 At special positions: 0 Unit cell: (86.52, 97.44, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 9 15.00 O 1349 8.00 N 1202 7.00 C 4621 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 3 sheets defined 43.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.653A pdb=" N LEU A 12 " --> pdb=" O HIS A 9 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 13 " --> pdb=" O GLN A 10 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 14 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS A 16 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 19 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.729A pdb=" N ARG A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.905A pdb=" N VAL A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.533A pdb=" N VAL B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.534A pdb=" N ILE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 removed outlier: 4.177A pdb=" N MET B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.797A pdb=" N ILE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 249 removed outlier: 3.729A pdb=" N ASN B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 247 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.695A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 266 " --> pdb=" O HIS B 262 " (cutoff:3.500A) Proline residue: B 269 - end of helix Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 313 through 334 removed outlier: 3.601A pdb=" N GLN B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.791A pdb=" N CYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR B 350 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.768A pdb=" N THR B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 391 removed outlier: 3.712A pdb=" N MET B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 386 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 389 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 390 " --> pdb=" O CYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 417 through 436 removed outlier: 3.890A pdb=" N SER B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 461 removed outlier: 3.522A pdb=" N ARG B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Proline residue: B 454 - end of helix removed outlier: 3.843A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 482 through 502 removed outlier: 3.787A pdb=" N HIS B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 532 removed outlier: 3.661A pdb=" N TRP B 511 " --> pdb=" O PRO B 508 " (cutoff:3.500A) Proline residue: B 512 - end of helix removed outlier: 4.313A pdb=" N PHE B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 516 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 519 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 521 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 522 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 523 " --> pdb=" O HIS B 520 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 524 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 526 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS B 528 " --> pdb=" O HIS B 525 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 529 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 530 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 531 " --> pdb=" O HIS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.654A pdb=" N THR B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 572 removed outlier: 3.507A pdb=" N LEU B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 572 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 585 through 595 removed outlier: 4.031A pdb=" N SER B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 610 through 621 removed outlier: 4.162A pdb=" N CYS B 615 " --> pdb=" O SER B 611 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 647 removed outlier: 3.536A pdb=" N ILE B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 630 " --> pdb=" O ASP B 626 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 635 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.589A pdb=" N ARG A 144 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG A 131 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 142 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 105 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU A 109 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N MET A 74 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 12.482A pdb=" N GLU A 111 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 14.142A pdb=" N ALA A 76 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 57 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 75 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.547A pdb=" N GLU C 63 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 113 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 72 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 84 " --> pdb=" O LEU C 75 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 489 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: 2.01 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1150 1.29 - 1.42: 1952 1.42 - 1.55: 4205 1.55 - 1.68: 18 1.68 - 1.81: 53 Bond restraints: 7378 Sorted by residual: bond pdb=" C1B CMC D 501 " pdb=" O4B CMC D 501 " ideal model delta sigma weight residual 1.656 1.389 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C GLY D 403 " pdb=" N PRO D 404 " ideal model delta sigma weight residual 1.341 1.496 -0.155 1.60e-02 3.91e+03 9.40e+01 bond pdb=" C1B CMC D 501 " pdb=" C2B CMC D 501 " ideal model delta sigma weight residual 1.326 1.515 -0.189 2.00e-02 2.50e+03 8.97e+01 bond pdb=" C9P CMC D 501 " pdb=" N8P CMC D 501 " ideal model delta sigma weight residual 1.481 1.306 0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" C5P CMC D 501 " pdb=" N4P CMC D 501 " ideal model delta sigma weight residual 1.468 1.310 0.158 2.00e-02 2.50e+03 6.27e+01 ... (remaining 7373 not shown) Histogram of bond angle deviations from ideal: 90.91 - 100.76: 20 100.76 - 110.61: 2323 110.61 - 120.47: 4964 120.47 - 130.32: 2665 130.32 - 140.17: 43 Bond angle restraints: 10015 Sorted by residual: angle pdb=" CA GLY D 403 " pdb=" C GLY D 403 " pdb=" N PRO D 404 " ideal model delta sigma weight residual 115.52 127.47 -11.95 1.13e+00 7.83e-01 1.12e+02 angle pdb=" CA GLN B 507 " pdb=" C GLN B 507 " pdb=" N PRO B 508 " ideal model delta sigma weight residual 118.45 127.91 -9.46 9.60e-01 1.09e+00 9.71e+01 angle pdb=" C GLN B 507 " pdb=" N PRO B 508 " pdb=" CA PRO B 508 " ideal model delta sigma weight residual 119.84 131.34 -11.50 1.25e+00 6.40e-01 8.47e+01 angle pdb=" O GLY D 403 " pdb=" C GLY D 403 " pdb=" N PRO D 404 " ideal model delta sigma weight residual 122.03 114.12 7.91 1.14e+00 7.69e-01 4.82e+01 angle pdb=" C GLU B 227 " pdb=" CA GLU B 227 " pdb=" CB GLU B 227 " ideal model delta sigma weight residual 109.75 121.64 -11.89 1.72e+00 3.38e-01 4.78e+01 ... (remaining 10010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3957 18.02 - 36.04: 374 36.04 - 54.06: 71 54.06 - 72.09: 10 72.09 - 90.11: 7 Dihedral angle restraints: 4419 sinusoidal: 1791 harmonic: 2628 Sorted by residual: dihedral pdb=" C GLU B 227 " pdb=" N GLU B 227 " pdb=" CA GLU B 227 " pdb=" CB GLU B 227 " ideal model delta harmonic sigma weight residual -122.60 -138.29 15.69 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" N LEU D 402 " pdb=" C LEU D 402 " pdb=" CA LEU D 402 " pdb=" CB LEU D 402 " ideal model delta harmonic sigma weight residual 122.80 107.46 15.34 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" CA PRO B 86 " pdb=" C PRO B 86 " pdb=" N LEU B 87 " pdb=" CA LEU B 87 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 4416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.913: 1130 0.913 - 1.827: 0 1.827 - 2.740: 0 2.740 - 3.654: 0 3.654 - 4.567: 4 Chirality restraints: 1134 Sorted by residual: chirality pdb=" C1 IHP A 301 " pdb=" C2 IHP A 301 " pdb=" C6 IHP A 301 " pdb=" O11 IHP A 301 " both_signs ideal model delta sigma weight residual False 2.32 -2.25 4.57 2.00e-01 2.50e+01 5.21e+02 chirality pdb=" C2 IHP A 301 " pdb=" C1 IHP A 301 " pdb=" C3 IHP A 301 " pdb=" O12 IHP A 301 " both_signs ideal model delta sigma weight residual False -2.52 1.77 -4.29 2.00e-01 2.50e+01 4.60e+02 chirality pdb=" C5 IHP A 301 " pdb=" C4 IHP A 301 " pdb=" C6 IHP A 301 " pdb=" O15 IHP A 301 " both_signs ideal model delta sigma weight residual False -2.42 1.84 -4.25 2.00e-01 2.50e+01 4.52e+02 ... (remaining 1131 not shown) Planarity restraints: 1254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P CMC D 501 " 0.212 2.00e-02 2.50e+03 1.76e-01 3.85e+02 pdb=" C5P CMC D 501 " -0.045 2.00e-02 2.50e+03 pdb=" C6P CMC D 501 " 0.147 2.00e-02 2.50e+03 pdb=" N4P CMC D 501 " -0.292 2.00e-02 2.50e+03 pdb=" O5P CMC D 501 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P CMC D 501 " 0.191 2.00e-02 2.50e+03 1.54e-01 2.98e+02 pdb=" C9P CMC D 501 " -0.087 2.00e-02 2.50e+03 pdb=" CAP CMC D 501 " 0.152 2.00e-02 2.50e+03 pdb=" N8P CMC D 501 " -0.226 2.00e-02 2.50e+03 pdb=" O9P CMC D 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 224 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C PHE B 224 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE B 224 " -0.023 2.00e-02 2.50e+03 pdb=" N SER B 225 " -0.020 2.00e-02 2.50e+03 ... (remaining 1251 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2393 2.83 - 3.35: 6213 3.35 - 3.87: 11256 3.87 - 4.38: 14315 4.38 - 4.90: 24013 Nonbonded interactions: 58190 Sorted by model distance: nonbonded pdb=" OE1 GLU B 386 " pdb=" OH TYR B 399 " model vdw 2.317 2.440 nonbonded pdb=" O HIS B 506 " pdb=" CZ3 TRP B 511 " model vdw 2.322 3.340 nonbonded pdb=" NH2 ARG A 69 " pdb=" O43 IHP A 301 " model vdw 2.328 2.520 nonbonded pdb=" O SER B 477 " pdb=" OG SER B 477 " model vdw 2.330 2.440 nonbonded pdb=" OD1 ASP B 105 " pdb=" OH TYR B 317 " model vdw 2.343 2.440 ... (remaining 58185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 36 5.16 5 C 4621 2.51 5 N 1202 2.21 5 O 1349 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=0.50 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 2.660 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 25.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 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 : 0.011 0.267 7378 Z= 0.719 Angle : 1.287 20.421 10015 Z= 0.660 Chirality : 0.266 4.567 1134 Planarity : 0.009 0.176 1254 Dihedral : 14.838 90.107 2715 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.76 % Favored : 89.90 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 2.70 % 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: -6.55 (0.18), residues: 874 helix: -4.83 (0.08), residues: 474 sheet: -3.29 (0.54), residues: 60 loop : -3.50 (0.28), residues: 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.822 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.2441 time to fit residues: 29.1835 Evaluate side-chains 70 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0732 time to fit residues: 1.4900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 296 GLN B 298 GLN B 332 ASN B 365 GLN B 402 ASN B 448 ASN B 451 ASN B 487 HIS B 507 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7378 Z= 0.179 Angle : 0.686 14.452 10015 Z= 0.340 Chirality : 0.049 0.683 1134 Planarity : 0.005 0.052 1254 Dihedral : 7.931 59.869 986 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -4.95 (0.23), residues: 874 helix: -3.39 (0.17), residues: 447 sheet: -2.65 (0.56), residues: 70 loop : -3.08 (0.29), residues: 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.806 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 81 average time/residue: 0.2511 time to fit residues: 26.2554 Evaluate side-chains 69 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0695 time to fit residues: 1.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 0.0470 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 7378 Z= 0.135 Angle : 0.585 7.746 10015 Z= 0.295 Chirality : 0.043 0.290 1134 Planarity : 0.004 0.049 1254 Dihedral : 7.166 57.489 986 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.25), residues: 874 helix: -2.33 (0.22), residues: 448 sheet: -2.36 (0.59), residues: 67 loop : -2.90 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.846 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 0.2272 time to fit residues: 24.1027 Evaluate side-chains 68 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1885 time to fit residues: 1.9638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 55 GLN B 298 GLN B 440 HIS B 448 ASN B 532 HIS ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7378 Z= 0.226 Angle : 0.607 7.808 10015 Z= 0.308 Chirality : 0.045 0.289 1134 Planarity : 0.004 0.051 1254 Dihedral : 6.820 56.860 986 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.26), residues: 874 helix: -1.93 (0.23), residues: 455 sheet: -2.16 (0.61), residues: 70 loop : -2.77 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.900 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.1932 time to fit residues: 20.7054 Evaluate side-chains 76 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0694 time to fit residues: 1.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7378 Z= 0.218 Angle : 0.596 7.889 10015 Z= 0.303 Chirality : 0.045 0.286 1134 Planarity : 0.004 0.052 1254 Dihedral : 6.669 55.633 986 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.27 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.27), residues: 874 helix: -1.64 (0.23), residues: 455 sheet: -2.02 (0.62), residues: 70 loop : -2.59 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.829 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.2028 time to fit residues: 21.8723 Evaluate side-chains 76 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0945 time to fit residues: 1.8910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN B 622 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7378 Z= 0.151 Angle : 0.564 9.230 10015 Z= 0.286 Chirality : 0.043 0.230 1134 Planarity : 0.004 0.049 1254 Dihedral : 6.484 57.046 986 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.28), residues: 874 helix: -1.28 (0.24), residues: 455 sheet: -1.87 (0.64), residues: 67 loop : -2.49 (0.32), residues: 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.873 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.2023 time to fit residues: 21.5954 Evaluate side-chains 73 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0684 time to fit residues: 1.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7378 Z= 0.149 Angle : 0.559 8.768 10015 Z= 0.283 Chirality : 0.042 0.217 1134 Planarity : 0.003 0.048 1254 Dihedral : 6.331 58.056 986 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.28), residues: 874 helix: -1.02 (0.24), residues: 458 sheet: -1.78 (0.64), residues: 67 loop : -2.46 (0.32), residues: 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.815 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.2134 time to fit residues: 22.5724 Evaluate side-chains 74 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0895 time to fit residues: 1.5452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 0.0270 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 ASN B 653 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7378 Z= 0.146 Angle : 0.555 8.791 10015 Z= 0.279 Chirality : 0.043 0.215 1134 Planarity : 0.003 0.048 1254 Dihedral : 6.245 56.956 986 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.28), residues: 874 helix: -0.79 (0.25), residues: 459 sheet: -1.87 (0.63), residues: 67 loop : -2.42 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.937 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.2038 time to fit residues: 21.8320 Evaluate side-chains 73 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0713 time to fit residues: 1.3178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN B 653 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7378 Z= 0.260 Angle : 0.627 9.524 10015 Z= 0.314 Chirality : 0.046 0.269 1134 Planarity : 0.004 0.049 1254 Dihedral : 6.477 55.020 986 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 874 helix: -0.86 (0.24), residues: 461 sheet: -1.88 (0.63), residues: 70 loop : -2.40 (0.32), residues: 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.899 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.1969 time to fit residues: 21.0845 Evaluate side-chains 76 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0902 time to fit residues: 1.8688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7378 Z= 0.141 Angle : 0.561 8.627 10015 Z= 0.284 Chirality : 0.043 0.194 1134 Planarity : 0.004 0.049 1254 Dihedral : 6.288 57.210 986 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 874 helix: -0.57 (0.25), residues: 459 sheet: -1.80 (0.65), residues: 65 loop : -2.36 (0.32), residues: 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.855 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.2271 time to fit residues: 23.8565 Evaluate side-chains 73 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0702 time to fit residues: 1.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0060 chunk 69 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089350 restraints weight = 24395.930| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.49 r_work: 0.2849 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 7378 Z= 0.120 Angle : 0.536 8.519 10015 Z= 0.270 Chirality : 0.041 0.181 1134 Planarity : 0.003 0.047 1254 Dihedral : 6.044 58.954 986 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.67 (0.29), residues: 874 helix: -0.21 (0.25), residues: 458 sheet: -1.68 (0.65), residues: 65 loop : -2.16 (0.33), residues: 351 =============================================================================== Job complete usr+sys time: 1599.08 seconds wall clock time: 29 minutes 46.08 seconds (1786.08 seconds total)