Starting phenix.real_space_refine on Mon Mar 11 14:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_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_23110/03_2024/7l1k_23110_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1k_23110/03_2024/7l1k_23110_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-5265/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: 6.57, per 1000 atoms: 0.91 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: 2.63 Conformation dependent library (CDL) restraints added in 2.1 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: 1.46 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: 1.80 Time building geometry restraints manager: 2.88 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=" 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=" C5P CMC D 501 " pdb=" N4P CMC D 501 " ideal model delta sigma weight residual 1.493 1.310 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C9P CMC D 501 " pdb=" N8P CMC D 501 " ideal model delta sigma weight residual 1.485 1.306 0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" C4B CMC D 501 " pdb=" O4B CMC D 501 " ideal model delta sigma weight residual 1.596 1.432 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" C3B CMC D 501 " pdb=" C4B CMC D 501 " ideal model delta sigma weight residual 1.347 1.495 -0.148 2.00e-02 2.50e+03 5.47e+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=" C1B CMC D 501 " pdb=" N9A CMC D 501 " pdb=" C4A CMC D 501 " ideal model delta sigma weight residual 90.87 125.04 -34.17 3.00e+00 1.11e-01 1.30e+02 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=" N1A CMC D 501 " pdb=" C6A CMC D 501 " pdb=" N6A CMC D 501 " ideal model delta sigma weight residual 94.05 118.71 -24.66 3.00e+00 1.11e-01 6.76e+01 ... (remaining 10010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 4323 33.10 - 66.20: 121 66.20 - 99.31: 13 99.31 - 132.41: 5 132.41 - 165.51: 1 Dihedral angle restraints: 4463 sinusoidal: 1835 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 4460 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 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: 0.570 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: 0.000 Extract box with map and model: 2.200 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.183 7378 Z= 0.705 Angle : 1.354 34.169 10015 Z= 0.675 Chirality : 0.266 4.567 1134 Planarity : 0.009 0.176 1254 Dihedral : 16.527 165.510 2759 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 % Allowed : 5.50 % Favored : 93.75 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 511 HIS 0.008 0.001 HIS B 506 PHE 0.015 0.002 PHE B 656 TYR 0.014 0.002 TYR A 129 ARG 0.003 0.000 ARG A 144 *********************** 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 : 0.770 Fit side-chains REVERT: A 41 GLU cc_start: 0.8061 (pm20) cc_final: 0.7748 (pm20) REVERT: A 123 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7933 (ttp80) REVERT: B 93 ARG cc_start: 0.8006 (ttt90) cc_final: 0.7731 (ttp80) REVERT: B 184 ASP cc_start: 0.8120 (t0) cc_final: 0.7863 (t0) REVERT: B 571 MET cc_start: 0.9038 (mtm) cc_final: 0.8808 (mtp) REVERT: B 660 TYR cc_start: 0.8511 (m-80) cc_final: 0.7879 (m-80) REVERT: C 78 ASP cc_start: 0.8963 (p0) cc_final: 0.8721 (p0) REVERT: C 80 GLU cc_start: 0.8557 (mp0) cc_final: 0.7986 (mp0) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.3150 time to fit residues: 36.6382 Evaluate side-chains 71 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 114 VAL 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: 0.6980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 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: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7378 Z= 0.201 Angle : 0.710 13.525 10015 Z= 0.347 Chirality : 0.048 0.594 1134 Planarity : 0.005 0.053 1254 Dihedral : 10.965 169.325 1036 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.84 % Favored : 91.04 % Rotamer: Outliers : 1.25 % Allowed : 8.88 % Favored : 89.88 % 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: -5.00 (0.22), residues: 874 helix: -3.41 (0.17), residues: 449 sheet: -2.66 (0.56), residues: 70 loop : -3.13 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 511 HIS 0.010 0.001 HIS B 334 PHE 0.012 0.001 PHE B 656 TYR 0.013 0.001 TYR B 509 ARG 0.007 0.001 ARG B 707 *********************** 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 90 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.825 Fit side-chains REVERT: A 118 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8172 (ptp) REVERT: A 123 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7881 (ttp80) REVERT: A 137 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 93 ARG cc_start: 0.7700 (ttt90) cc_final: 0.7497 (ttp80) REVERT: B 188 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7458 (tp) REVERT: B 227 GLU cc_start: 0.7443 (pt0) cc_final: 0.7201 (tm-30) REVERT: B 378 ASP cc_start: 0.8221 (p0) cc_final: 0.7807 (p0) REVERT: B 467 ASP cc_start: 0.7752 (m-30) cc_final: 0.7536 (m-30) REVERT: B 571 MET cc_start: 0.9111 (mtm) cc_final: 0.8894 (mtt) REVERT: B 660 TYR cc_start: 0.8408 (m-80) cc_final: 0.7870 (m-80) REVERT: C 80 GLU cc_start: 0.8571 (mp0) cc_final: 0.8124 (mp0) outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.2675 time to fit residues: 29.0300 Evaluate side-chains 75 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 114 VAL 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: 1.9990 chunk 53 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 532 HIS 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: 0.8321 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7378 Z= 0.172 Angle : 0.607 9.488 10015 Z= 0.306 Chirality : 0.044 0.303 1134 Planarity : 0.004 0.051 1254 Dihedral : 9.906 163.361 1031 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.18 % Favored : 90.70 % Rotamer: Outliers : 1.75 % Allowed : 10.50 % Favored : 87.75 % 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: -3.94 (0.25), residues: 874 helix: -2.33 (0.22), residues: 448 sheet: -2.32 (0.60), residues: 70 loop : -2.89 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 511 HIS 0.008 0.001 HIS B 334 PHE 0.011 0.001 PHE B 177 TYR 0.010 0.001 TYR B 509 ARG 0.007 0.000 ARG B 707 *********************** 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 87 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.840 Fit side-chains REVERT: A 123 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7947 (ttp80) REVERT: A 137 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7577 (pp) REVERT: B 188 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7518 (tp) REVERT: B 378 ASP cc_start: 0.8186 (p0) cc_final: 0.7827 (p0) REVERT: B 467 ASP cc_start: 0.7654 (m-30) cc_final: 0.7264 (m-30) REVERT: B 519 ASP cc_start: 0.8217 (p0) cc_final: 0.7890 (t0) REVERT: B 571 MET cc_start: 0.9067 (mtm) cc_final: 0.8809 (mtp) REVERT: B 660 TYR cc_start: 0.8385 (m-80) cc_final: 0.7853 (m-80) REVERT: C 78 ASP cc_start: 0.8852 (p0) cc_final: 0.8645 (p0) REVERT: C 80 GLU cc_start: 0.8390 (mp0) cc_final: 0.7713 (mp0) outliers start: 14 outliers final: 7 residues processed: 81 average time/residue: 0.2352 time to fit residues: 24.9871 Evaluate side-chains 75 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 HIS B 448 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: 0.8332 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7378 Z= 0.208 Angle : 0.611 9.103 10015 Z= 0.309 Chirality : 0.044 0.256 1134 Planarity : 0.004 0.051 1254 Dihedral : 9.706 164.046 1031 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.62 % Allowed : 11.12 % Favored : 87.25 % 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: -3.48 (0.26), residues: 874 helix: -1.88 (0.23), residues: 453 sheet: -2.10 (0.61), residues: 70 loop : -2.80 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 511 HIS 0.008 0.001 HIS B 334 PHE 0.014 0.001 PHE B 656 TYR 0.010 0.001 TYR A 129 ARG 0.009 0.000 ARG B 707 *********************** 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 84 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.747 Fit side-chains REVERT: A 123 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7960 (ttp80) REVERT: A 137 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7575 (pp) REVERT: B 78 MET cc_start: 0.8847 (mmt) cc_final: 0.8215 (mmt) REVERT: B 188 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7580 (tp) REVERT: B 378 ASP cc_start: 0.8161 (p0) cc_final: 0.7763 (p0) REVERT: B 519 ASP cc_start: 0.8222 (p0) cc_final: 0.7899 (t0) REVERT: B 571 MET cc_start: 0.9071 (mtm) cc_final: 0.8811 (mtp) REVERT: B 593 MET cc_start: 0.8446 (tpt) cc_final: 0.8223 (tpt) REVERT: B 660 TYR cc_start: 0.8391 (m-80) cc_final: 0.7855 (m-80) REVERT: C 80 GLU cc_start: 0.8410 (mp0) cc_final: 0.7764 (mp0) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.1980 time to fit residues: 20.7431 Evaluate side-chains 80 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 298 GLN B 379 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7378 Z= 0.307 Angle : 0.663 9.063 10015 Z= 0.334 Chirality : 0.047 0.312 1134 Planarity : 0.004 0.053 1254 Dihedral : 9.841 166.831 1031 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.88 % Allowed : 12.38 % Favored : 85.75 % 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: -3.27 (0.27), residues: 874 helix: -1.74 (0.23), residues: 457 sheet: -1.86 (0.64), residues: 68 loop : -2.71 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 39 HIS 0.008 0.001 HIS B 334 PHE 0.020 0.001 PHE B 656 TYR 0.013 0.001 TYR A 7 ARG 0.007 0.000 ARG B 707 *********************** 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 88 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.849 Fit side-chains REVERT: A 137 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7585 (pp) REVERT: B 55 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: B 188 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7632 (tp) REVERT: B 378 ASP cc_start: 0.8195 (p0) cc_final: 0.7791 (p0) REVERT: B 593 MET cc_start: 0.8499 (tpt) cc_final: 0.8271 (tpt) REVERT: B 660 TYR cc_start: 0.8422 (m-80) cc_final: 0.7850 (m-80) REVERT: C 78 ASP cc_start: 0.8908 (p0) cc_final: 0.8694 (p0) REVERT: C 80 GLU cc_start: 0.8369 (mp0) cc_final: 0.7671 (mp0) outliers start: 15 outliers final: 9 residues processed: 82 average time/residue: 0.1991 time to fit residues: 22.4030 Evaluate side-chains 81 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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** B 379 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: 0.8317 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7378 Z= 0.174 Angle : 0.598 8.982 10015 Z= 0.302 Chirality : 0.044 0.235 1134 Planarity : 0.004 0.051 1254 Dihedral : 9.518 165.415 1031 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.25 % Allowed : 14.00 % Favored : 84.75 % 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: -2.89 (0.28), residues: 874 helix: -1.36 (0.24), residues: 453 sheet: -1.84 (0.65), residues: 67 loop : -2.59 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 511 HIS 0.007 0.001 HIS B 334 PHE 0.011 0.001 PHE B 177 TYR 0.010 0.001 TYR B 509 ARG 0.008 0.000 ARG B 707 *********************** 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 83 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.863 Fit side-chains REVERT: A 137 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7521 (pp) REVERT: B 188 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7596 (tp) REVERT: B 378 ASP cc_start: 0.8185 (p0) cc_final: 0.7768 (p0) REVERT: B 519 ASP cc_start: 0.8271 (p0) cc_final: 0.7979 (t0) REVERT: B 593 MET cc_start: 0.8455 (tpt) cc_final: 0.8208 (tpt) REVERT: B 660 TYR cc_start: 0.8362 (m-80) cc_final: 0.7881 (m-80) REVERT: C 78 ASP cc_start: 0.8961 (p0) cc_final: 0.8721 (p0) REVERT: C 80 GLU cc_start: 0.8331 (mp0) cc_final: 0.7768 (mp0) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.1897 time to fit residues: 19.8836 Evaluate side-chains 80 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** B 379 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: 0.8298 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7378 Z= 0.166 Angle : 0.581 8.755 10015 Z= 0.293 Chirality : 0.043 0.230 1134 Planarity : 0.003 0.049 1254 Dihedral : 9.235 161.608 1031 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.62 % Allowed : 14.25 % Favored : 84.12 % 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: -2.67 (0.28), residues: 874 helix: -1.16 (0.24), residues: 459 sheet: -1.86 (0.64), residues: 70 loop : -2.48 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 511 HIS 0.007 0.001 HIS B 334 PHE 0.011 0.001 PHE B 177 TYR 0.010 0.001 TYR A 129 ARG 0.009 0.000 ARG B 707 *********************** 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 91 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.859 Fit side-chains REVERT: A 29 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8111 (tttt) REVERT: A 137 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7474 (pp) REVERT: B 378 ASP cc_start: 0.8160 (p0) cc_final: 0.7750 (p0) REVERT: B 593 MET cc_start: 0.8481 (tpt) cc_final: 0.8241 (tpt) REVERT: B 660 TYR cc_start: 0.8314 (m-80) cc_final: 0.7824 (m-80) REVERT: B 693 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7955 (mmmt) REVERT: C 80 GLU cc_start: 0.8295 (mp0) cc_final: 0.7889 (mp0) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.2000 time to fit residues: 22.5902 Evaluate side-chains 82 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN B 451 ASN B 653 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2459 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= 0.157 Angle : 0.573 8.741 10015 Z= 0.289 Chirality : 0.043 0.225 1134 Planarity : 0.003 0.049 1254 Dihedral : 9.048 158.591 1031 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 1.75 % Allowed : 14.50 % Favored : 83.75 % 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: -2.46 (0.28), residues: 874 helix: -0.95 (0.24), residues: 459 sheet: -1.81 (0.65), residues: 67 loop : -2.44 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 511 HIS 0.002 0.000 HIS B 506 PHE 0.009 0.001 PHE B 656 TYR 0.009 0.001 TYR B 509 ARG 0.009 0.000 ARG B 707 *********************** 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 91 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.861 Fit side-chains REVERT: A 29 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8127 (tttt) REVERT: A 137 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7477 (pp) REVERT: B 378 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 380 PRO cc_start: 0.8089 (Cg_endo) cc_final: 0.7860 (Cg_exo) REVERT: B 436 ARG cc_start: 0.8389 (tmm160) cc_final: 0.7999 (ttp80) REVERT: B 593 MET cc_start: 0.8474 (tpt) cc_final: 0.8247 (tpt) REVERT: B 660 TYR cc_start: 0.8280 (m-80) cc_final: 0.7781 (m-80) REVERT: B 693 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7985 (mmmt) REVERT: C 78 ASP cc_start: 0.8950 (p0) cc_final: 0.8564 (p0) REVERT: C 80 GLU cc_start: 0.8240 (mp0) cc_final: 0.7688 (mp0) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.2285 time to fit residues: 24.8758 Evaluate side-chains 87 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7378 Z= 0.174 Angle : 0.581 8.736 10015 Z= 0.292 Chirality : 0.043 0.226 1134 Planarity : 0.003 0.048 1254 Dihedral : 8.991 156.402 1031 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 1.62 % Allowed : 14.25 % Favored : 84.12 % 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: -2.30 (0.28), residues: 874 helix: -0.79 (0.25), residues: 459 sheet: -1.79 (0.65), residues: 67 loop : -2.40 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 511 HIS 0.002 0.001 HIS C 108 PHE 0.011 0.001 PHE B 656 TYR 0.009 0.001 TYR A 129 ARG 0.009 0.000 ARG B 707 *********************** 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 90 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.890 Fit side-chains REVERT: A 29 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8119 (tttt) REVERT: A 137 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7484 (pp) REVERT: B 378 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 380 PRO cc_start: 0.8110 (Cg_endo) cc_final: 0.7889 (Cg_exo) REVERT: B 436 ARG cc_start: 0.8380 (tmm160) cc_final: 0.7988 (ttp80) REVERT: B 593 MET cc_start: 0.8461 (tpt) cc_final: 0.8209 (tpt) REVERT: B 660 TYR cc_start: 0.8297 (m-80) cc_final: 0.7800 (m-80) REVERT: B 693 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8020 (mmmt) REVERT: C 78 ASP cc_start: 0.8949 (p0) cc_final: 0.8566 (p0) REVERT: C 80 GLU cc_start: 0.8241 (mp0) cc_final: 0.7645 (mp0) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.2153 time to fit residues: 23.4146 Evaluate side-chains 86 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 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: 0.8282 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7378 Z= 0.170 Angle : 0.575 8.763 10015 Z= 0.290 Chirality : 0.043 0.223 1134 Planarity : 0.003 0.049 1254 Dihedral : 8.880 152.916 1031 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % 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: -2.11 (0.28), residues: 874 helix: -0.62 (0.25), residues: 459 sheet: -1.62 (0.65), residues: 65 loop : -2.36 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 511 HIS 0.002 0.001 HIS C 108 PHE 0.011 0.001 PHE B 656 TYR 0.009 0.001 TYR A 129 ARG 0.009 0.000 ARG B 707 ********************** 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 90 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.878 Fit side-chains REVERT: A 29 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8116 (tttt) REVERT: A 137 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7489 (pp) REVERT: B 378 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7644 (p0) REVERT: B 380 PRO cc_start: 0.8094 (Cg_endo) cc_final: 0.7880 (Cg_exo) REVERT: B 436 ARG cc_start: 0.8387 (tmm160) cc_final: 0.7995 (ttp80) REVERT: B 593 MET cc_start: 0.8462 (tpt) cc_final: 0.8211 (tpt) REVERT: B 660 TYR cc_start: 0.8295 (m-80) cc_final: 0.7719 (m-80) REVERT: B 693 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8027 (mmmt) REVERT: C 80 GLU cc_start: 0.8230 (mp0) cc_final: 0.7711 (mp0) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.2643 time to fit residues: 29.1150 Evaluate side-chains 86 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** 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 = 0.3250 r_free = 0.3250 target = 0.104692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.087270 restraints weight = 24340.015| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.42 r_work: 0.2811 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2686 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= 0.135 Angle : 0.553 8.673 10015 Z= 0.278 Chirality : 0.042 0.200 1134 Planarity : 0.003 0.048 1254 Dihedral : 8.596 147.570 1031 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.62 % Allowed : 14.50 % Favored : 83.88 % 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: -1.89 (0.29), residues: 874 helix: -0.39 (0.25), residues: 457 sheet: -1.70 (0.64), residues: 67 loop : -2.28 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 511 HIS 0.002 0.000 HIS B 440 PHE 0.008 0.001 PHE B 445 TYR 0.010 0.001 TYR B 509 ARG 0.009 0.000 ARG B 707 =============================================================================== Job complete usr+sys time: 1753.14 seconds wall clock time: 32 minutes 29.82 seconds (1949.82 seconds total)