Starting phenix.real_space_refine on Sun Mar 17 10:06:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shf_25126/03_2024/7shf_25126_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 5953 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 2 5.49 5 S 67 5.16 5 C 7608 2.51 5 N 1808 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11443 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3329 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3318 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 374} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 400, 3318 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 374} Chain breaks: 1 bond proxies already assigned to first conformer: 3394 Chain: "D" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2660 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 339} Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2322 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2412 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 280 Unusual residues: {'CLR': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 440 Unusual residues: {'CLR': 12, 'EIJ': 1, 'PEE': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 271 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG C 271 " occ=0.54 Time building chain proxies: 8.07, per 1000 atoms: 0.71 Number of scatterers: 11443 At special positions: 0 Unit cell: (79.443, 109.125, 184.203, 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 67 16.00 P 2 15.00 O 1958 8.00 N 1808 7.00 C 7608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 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: 3.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 9 sheets defined 43.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.659A pdb=" N LYS C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.739A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.735A pdb=" N ALA C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.523A pdb=" N GLU C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 179 Processing helix chain 'C' and resid 184 through 191 removed outlier: 3.634A pdb=" N ASP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.572A pdb=" N GLN C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 293 removed outlier: 3.587A pdb=" N TYR C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR C 293 " --> pdb=" O GLN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 311 through 317 Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.871A pdb=" N GLY C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 332 " --> pdb=" O LYS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.601A pdb=" N VAL C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 367 " --> pdb=" O TRP C 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 388 Proline residue: C 378 - end of helix removed outlier: 4.041A pdb=" N VAL C 381 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 382 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 387 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 388 " --> pdb=" O TRP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.575A pdb=" N LEU C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'D' and resid 9 through 33 Processing helix chain 'D' and resid 38 through 44 removed outlier: 5.650A pdb=" N ARG D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 145 No H-bonds generated for 'chain 'D' and resid 142 through 145' Processing helix chain 'B' and resid 417 through 441 removed outlier: 3.777A pdb=" N ILE B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.975A pdb=" N SER B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 458 through 470 removed outlier: 4.609A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 489 through 502 removed outlier: 4.391A pdb=" N THR B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.980A pdb=" N THR B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 529 No H-bonds generated for 'chain 'B' and resid 526 through 529' Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.593A pdb=" N VAL B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 578 through 585 removed outlier: 3.761A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.664A pdb=" N TYR B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 612 No H-bonds generated for 'chain 'B' and resid 609 through 612' Processing helix chain 'B' and resid 616 through 633 removed outlier: 4.596A pdb=" N LEU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 651 removed outlier: 3.519A pdb=" N LEU B 646 " --> pdb=" O TRP B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 713 through 729 removed outlier: 3.776A pdb=" N LYS B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 4.607A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 459 removed outlier: 4.375A pdb=" N THR A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.826A pdb=" N LEU A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 530 through 547 removed outlier: 3.520A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.572A pdb=" N PHE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 615 through 633 removed outlier: 4.020A pdb=" N GLU A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.849A pdb=" N ILE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG A 715 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 91 through 93 Processing sheet with id= B, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.896A pdb=" N SER D 81 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET D 69 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 79 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP D 71 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG D 77 " --> pdb=" O TRP D 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 78 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP D 91 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS D 97 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.559A pdb=" N ALA D 150 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 131 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER D 148 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 156 through 161 removed outlier: 6.889A pdb=" N ALA D 171 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N CYS D 159 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 169 " --> pdb=" O CYS D 159 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE D 161 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLN D 167 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 189 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP D 181 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 187 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 233 through 235 removed outlier: 3.782A pdb=" N GLN D 233 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 223 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 212 " --> pdb=" O TRP D 224 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.749A pdb=" N ALA D 275 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 254 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 286 through 291 removed outlier: 6.568A pdb=" N GLY D 301 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 289 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE D 299 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE D 291 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU D 297 " --> pdb=" O PHE D 291 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER D 319 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP D 311 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG D 317 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 340 through 343 removed outlier: 3.615A pdb=" N ARG D 350 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA D 353 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR D 55 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 559 through 563 308 hydrogen bonds defined for protein. 879 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: 2.94 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1698 1.30 - 1.43: 3042 1.43 - 1.56: 6883 1.56 - 1.68: 38 1.68 - 1.81: 106 Bond restraints: 11767 Sorted by residual: bond pdb=" C05 EIJ A 813 " pdb=" C06 EIJ A 813 " ideal model delta sigma weight residual 1.556 1.329 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C08 EIJ A 813 " pdb=" C09 EIJ A 813 " ideal model delta sigma weight residual 1.558 1.338 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C03 EIJ A 813 " pdb=" C04 EIJ A 813 " ideal model delta sigma weight residual 1.321 1.533 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C24 PEE A 814 " pdb=" C25 PEE A 814 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C06 EIJ A 813 " pdb=" C07 EIJ A 813 " ideal model delta sigma weight residual 1.348 1.539 -0.191 2.00e-02 2.50e+03 9.09e+01 ... (remaining 11762 not shown) Histogram of bond angle deviations from ideal: 97.75 - 108.94: 925 108.94 - 120.14: 10432 120.14 - 131.34: 4650 131.34 - 142.53: 37 142.53 - 153.73: 3 Bond angle restraints: 16047 Sorted by residual: angle pdb=" C07 EIJ A 813 " pdb=" C08 EIJ A 813 " pdb=" C09 EIJ A 813 " ideal model delta sigma weight residual 109.49 153.73 -44.24 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C12 EIJ A 813 " pdb=" C13 EIJ A 813 " pdb=" C14 EIJ A 813 " ideal model delta sigma weight residual 152.67 111.76 40.91 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C09 EIJ A 813 " pdb=" C10 EIJ A 813 " pdb=" C11 EIJ A 813 " ideal model delta sigma weight residual 152.66 112.13 40.53 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C06 EIJ A 813 " pdb=" C07 EIJ A 813 " pdb=" C08 EIJ A 813 " ideal model delta sigma weight residual 152.64 112.74 39.90 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C21 PEE A 814 " pdb=" C22 PEE A 814 " pdb=" C23 PEE A 814 " ideal model delta sigma weight residual 113.44 152.74 -39.30 3.00e+00 1.11e-01 1.72e+02 ... (remaining 16042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 7696 35.58 - 71.16: 304 71.16 - 106.74: 44 106.74 - 142.32: 11 142.32 - 177.90: 2 Dihedral angle restraints: 8057 sinusoidal: 4149 harmonic: 3908 Sorted by residual: dihedral pdb=" CB CYS A 481 " pdb=" SG CYS A 481 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual 93.00 168.86 -75.86 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS B 481 " pdb=" SG CYS B 481 " pdb=" SG CYS B 573 " pdb=" CB CYS B 573 " ideal model delta sinusoidal sigma weight residual 93.00 167.20 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" C3 PEE A 814 " pdb=" C1 PEE A 814 " pdb=" C2 PEE A 814 " pdb=" O3P PEE A 814 " ideal model delta sinusoidal sigma weight residual 62.73 -115.17 177.90 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1838 1.009 - 2.018: 0 2.018 - 3.027: 0 3.027 - 4.036: 0 4.036 - 5.045: 9 Chirality restraints: 1847 Sorted by residual: chirality pdb=" C17 CLR A 809 " pdb=" C13 CLR A 809 " pdb=" C16 CLR A 809 " pdb=" C20 CLR A 809 " both_signs ideal model delta sigma weight residual False 2.55 -2.49 5.05 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C47 EIJ A 813 " pdb=" C46 EIJ A 813 " pdb=" C49 EIJ A 813 " pdb=" O48 EIJ A 813 " both_signs ideal model delta sigma weight residual False 2.51 -2.53 5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C55 EIJ A 813 " pdb=" C46 EIJ A 813 " pdb=" C53 EIJ A 813 " pdb=" O56 EIJ A 813 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.34e+02 ... (remaining 1844 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIJ A 813 " 0.164 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C12 EIJ A 813 " -0.454 2.00e-02 2.50e+03 pdb=" C13 EIJ A 813 " 0.442 2.00e-02 2.50e+03 pdb=" C14 EIJ A 813 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 EIJ A 813 " -0.103 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C03 EIJ A 813 " 0.105 2.00e-02 2.50e+03 pdb=" C04 EIJ A 813 " 0.100 2.00e-02 2.50e+03 pdb=" C05 EIJ A 813 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EIJ A 813 " -0.070 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C06 EIJ A 813 " 0.076 2.00e-02 2.50e+03 pdb=" C07 EIJ A 813 " 0.050 2.00e-02 2.50e+03 pdb=" C08 EIJ A 813 " -0.057 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 756 2.73 - 3.27: 11175 3.27 - 3.82: 16938 3.82 - 4.36: 22268 4.36 - 4.90: 36840 Nonbonded interactions: 87977 Sorted by model distance: nonbonded pdb=" OD1 ASP D 346 " pdb=" OG1 THR D 348 " model vdw 2.190 2.440 nonbonded pdb=" OD1 ASP D 304 " pdb=" OG1 THR D 306 " model vdw 2.198 2.440 nonbonded pdb=" O ARG A 715 " pdb=" NZ LYS A 719 " model vdw 2.245 2.520 nonbonded pdb=" O CYS A 481 " pdb=" NH1 ARG A 485 " model vdw 2.250 2.520 nonbonded pdb=" CE2 PHE B 460 " pdb=" C23 CLR B 803 " model vdw 2.258 3.740 ... (remaining 87972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 406 through 670 or resid 712 through 730 or resid 805 thro \ ugh 812)) selection = (chain 'B' and ((resid 406 through 408 and (name N or name CA or name C or name \ O or name CB )) or resid 409 through 730 or resid 801 through 808)) } 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=0.46 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 13.380 Check model and map are aligned: 0.180 Set scattering table: 0.090 Process input model: 33.370 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.008 0.227 11767 Z= 0.434 Angle : 1.144 44.238 16047 Z= 0.518 Chirality : 0.346 5.045 1847 Planarity : 0.010 0.336 1862 Dihedral : 18.426 177.905 5515 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.09 % Favored : 92.38 % Rotamer: Outliers : 0.68 % Allowed : 0.43 % Favored : 98.89 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % 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: -3.05 (0.22), residues: 1315 helix: -2.50 (0.18), residues: 665 sheet: -0.78 (0.45), residues: 137 loop : -1.42 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 65 HIS 0.006 0.001 HIS D 347 PHE 0.034 0.002 PHE A 474 TYR 0.044 0.002 TYR A 496 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: C 186 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: C 276 MET cc_start: 0.7076 (mmp) cc_final: 0.6629 (tpt) REVERT: C 281 ASP cc_start: 0.8265 (m-30) cc_final: 0.7838 (m-30) REVERT: C 386 GLN cc_start: 0.8952 (mt0) cc_final: 0.8512 (tp40) REVERT: D 46 GLU cc_start: 0.7821 (pm20) cc_final: 0.6782 (mm-30) REVERT: D 166 MET cc_start: 0.8189 (mmt) cc_final: 0.7814 (mmm) REVERT: B 418 LEU cc_start: 0.6701 (pt) cc_final: 0.6186 (tp) REVERT: B 529 MET cc_start: 0.8152 (mtp) cc_final: 0.7946 (mtt) REVERT: B 620 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 445 LYS cc_start: 0.8613 (mtpt) cc_final: 0.7816 (mmpt) REVERT: A 716 ASP cc_start: 0.7674 (t0) cc_final: 0.7024 (m-30) outliers start: 8 outliers final: 3 residues processed: 175 average time/residue: 0.2427 time to fit residues: 60.3494 Evaluate side-chains 138 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11767 Z= 0.187 Angle : 0.666 9.747 16047 Z= 0.317 Chirality : 0.043 0.273 1847 Planarity : 0.005 0.073 1862 Dihedral : 13.303 149.333 2966 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 0.77 % Allowed : 7.69 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.49 (0.22), residues: 1315 helix: -1.98 (0.19), residues: 675 sheet: -0.58 (0.42), residues: 144 loop : -1.19 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 PHE 0.015 0.001 PHE B 510 TYR 0.023 0.002 TYR A 496 ARG 0.004 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: C 276 MET cc_start: 0.6692 (mmp) cc_final: 0.6217 (tpt) REVERT: C 281 ASP cc_start: 0.8155 (m-30) cc_final: 0.7722 (m-30) REVERT: C 334 MET cc_start: 0.8901 (ttm) cc_final: 0.8518 (ttp) REVERT: D 46 GLU cc_start: 0.7812 (pm20) cc_final: 0.6793 (mm-30) REVERT: D 142 MET cc_start: 0.6328 (mpp) cc_final: 0.5571 (mtm) REVERT: D 166 MET cc_start: 0.8106 (mmt) cc_final: 0.7796 (mmm) REVERT: B 428 MET cc_start: 0.8321 (mtm) cc_final: 0.7972 (mtm) REVERT: B 445 LYS cc_start: 0.8108 (tppt) cc_final: 0.7262 (tptt) REVERT: B 620 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6506 (tm-30) REVERT: B 624 SER cc_start: 0.8969 (t) cc_final: 0.8532 (p) REVERT: A 445 LYS cc_start: 0.8610 (mtpt) cc_final: 0.7808 (mmpt) REVERT: A 716 ASP cc_start: 0.7716 (t0) cc_final: 0.7097 (m-30) outliers start: 9 outliers final: 7 residues processed: 149 average time/residue: 0.2364 time to fit residues: 51.1672 Evaluate side-chains 142 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS A 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11767 Z= 0.275 Angle : 0.653 10.264 16047 Z= 0.319 Chirality : 0.044 0.308 1847 Planarity : 0.005 0.063 1862 Dihedral : 11.604 137.920 2966 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.24 % Favored : 92.30 % Rotamer: Outliers : 1.20 % Allowed : 9.91 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.23), residues: 1315 helix: -1.73 (0.19), residues: 685 sheet: -0.84 (0.41), residues: 160 loop : -1.10 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 65 HIS 0.006 0.001 HIS D 347 PHE 0.020 0.002 PHE C 91 TYR 0.023 0.002 TYR A 496 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: C 276 MET cc_start: 0.6704 (mmp) cc_final: 0.6271 (tpt) REVERT: C 334 MET cc_start: 0.8966 (ttm) cc_final: 0.8676 (ttp) REVERT: D 46 GLU cc_start: 0.7815 (pm20) cc_final: 0.6794 (mm-30) REVERT: D 166 MET cc_start: 0.8141 (mmt) cc_final: 0.7826 (mmm) REVERT: D 226 MET cc_start: 0.8735 (mtp) cc_final: 0.8365 (mmm) REVERT: B 414 LYS cc_start: 0.5963 (tppt) cc_final: 0.4846 (tmtt) REVERT: B 428 MET cc_start: 0.8318 (mtm) cc_final: 0.8022 (mtm) REVERT: B 445 LYS cc_start: 0.8242 (tppt) cc_final: 0.7627 (mmmt) REVERT: B 620 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 623 ILE cc_start: 0.8914 (tt) cc_final: 0.8680 (tt) REVERT: A 642 TRP cc_start: 0.7181 (m-10) cc_final: 0.6979 (m-90) REVERT: A 716 ASP cc_start: 0.7656 (t0) cc_final: 0.7016 (m-30) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.2303 time to fit residues: 48.7503 Evaluate side-chains 138 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 34 optimal weight: 7.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN A 504 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11767 Z= 0.153 Angle : 0.556 10.007 16047 Z= 0.272 Chirality : 0.040 0.246 1847 Planarity : 0.004 0.062 1862 Dihedral : 10.676 132.795 2960 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.64 % Favored : 93.90 % Rotamer: Outliers : 1.11 % Allowed : 11.36 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.95 (0.23), residues: 1315 helix: -1.42 (0.20), residues: 677 sheet: -0.62 (0.41), residues: 158 loop : -1.01 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 65 HIS 0.004 0.001 HIS D 347 PHE 0.016 0.001 PHE C 350 TYR 0.024 0.001 TYR A 598 ARG 0.002 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: C 276 MET cc_start: 0.6720 (mmp) cc_final: 0.6299 (tpt) REVERT: C 334 MET cc_start: 0.8859 (ttm) cc_final: 0.8604 (ttp) REVERT: D 46 GLU cc_start: 0.7796 (pm20) cc_final: 0.6810 (mm-30) REVERT: D 166 MET cc_start: 0.8167 (mmt) cc_final: 0.7861 (mmm) REVERT: D 202 ASP cc_start: 0.8490 (t0) cc_final: 0.8131 (t70) REVERT: D 226 MET cc_start: 0.8710 (mtp) cc_final: 0.8329 (mmm) REVERT: B 414 LYS cc_start: 0.5864 (tppt) cc_final: 0.4813 (tmtt) REVERT: B 428 MET cc_start: 0.8214 (mtm) cc_final: 0.7968 (mtm) REVERT: B 445 LYS cc_start: 0.8154 (tppt) cc_final: 0.7313 (tptp) REVERT: B 620 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6650 (tm-30) REVERT: B 623 ILE cc_start: 0.8759 (tt) cc_final: 0.8545 (tt) REVERT: A 642 TRP cc_start: 0.7146 (m-10) cc_final: 0.6939 (m-90) REVERT: A 716 ASP cc_start: 0.7697 (t0) cc_final: 0.7104 (m-30) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.2203 time to fit residues: 49.6186 Evaluate side-chains 140 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 31 optimal weight: 10.0000 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11767 Z= 0.206 Angle : 0.586 10.512 16047 Z= 0.284 Chirality : 0.041 0.210 1847 Planarity : 0.004 0.065 1862 Dihedral : 10.562 131.421 2960 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 1.62 % Allowed : 12.21 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.82 (0.23), residues: 1315 helix: -1.24 (0.20), residues: 676 sheet: -0.70 (0.41), residues: 160 loop : -1.03 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 PHE 0.017 0.001 PHE C 350 TYR 0.019 0.001 TYR A 598 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: C 276 MET cc_start: 0.6773 (mmp) cc_final: 0.6351 (tpt) REVERT: C 334 MET cc_start: 0.8912 (ttm) cc_final: 0.8698 (ttp) REVERT: D 46 GLU cc_start: 0.7813 (pm20) cc_final: 0.6821 (mm-30) REVERT: D 166 MET cc_start: 0.8196 (mmt) cc_final: 0.7849 (mmm) REVERT: D 202 ASP cc_start: 0.8484 (t0) cc_final: 0.7950 (t0) REVERT: B 414 LYS cc_start: 0.5982 (tppt) cc_final: 0.4882 (tmtt) REVERT: B 428 MET cc_start: 0.8235 (mtm) cc_final: 0.7994 (mtm) REVERT: B 620 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6782 (tm-30) REVERT: B 623 ILE cc_start: 0.8786 (tt) cc_final: 0.8580 (tt) REVERT: B 639 GLN cc_start: 0.7459 (mt0) cc_final: 0.6981 (mt0) REVERT: A 642 TRP cc_start: 0.7148 (m-10) cc_final: 0.6895 (m-90) REVERT: A 715 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7326 (mtp180) REVERT: A 716 ASP cc_start: 0.7758 (t0) cc_final: 0.7154 (m-30) outliers start: 19 outliers final: 14 residues processed: 145 average time/residue: 0.2428 time to fit residues: 51.1731 Evaluate side-chains 140 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11767 Z= 0.182 Angle : 0.567 11.119 16047 Z= 0.276 Chirality : 0.040 0.176 1847 Planarity : 0.004 0.068 1862 Dihedral : 10.234 129.036 2960 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.40 % Favored : 93.14 % Rotamer: Outliers : 1.37 % Allowed : 13.58 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.66 (0.23), residues: 1315 helix: -1.10 (0.20), residues: 675 sheet: -0.69 (0.41), residues: 162 loop : -0.94 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 PHE 0.018 0.001 PHE C 350 TYR 0.017 0.001 TYR A 598 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: C 198 ASP cc_start: 0.6811 (m-30) cc_final: 0.6562 (m-30) REVERT: C 276 MET cc_start: 0.6785 (mmp) cc_final: 0.6356 (tpt) REVERT: D 46 GLU cc_start: 0.7813 (pm20) cc_final: 0.6808 (mm-30) REVERT: D 166 MET cc_start: 0.8189 (mmt) cc_final: 0.7907 (mmm) REVERT: D 202 ASP cc_start: 0.8483 (t0) cc_final: 0.7963 (t0) REVERT: D 226 MET cc_start: 0.8717 (mtp) cc_final: 0.8344 (mmm) REVERT: B 414 LYS cc_start: 0.5999 (tppt) cc_final: 0.4906 (tmtt) REVERT: B 620 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6819 (tm-30) REVERT: A 538 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7170 (t80) REVERT: A 598 TYR cc_start: 0.8414 (t80) cc_final: 0.8212 (t80) REVERT: A 642 TRP cc_start: 0.7150 (m-10) cc_final: 0.6885 (m-90) REVERT: A 715 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7292 (mtp180) REVERT: A 716 ASP cc_start: 0.7770 (t0) cc_final: 0.7197 (m-30) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.2387 time to fit residues: 48.5656 Evaluate side-chains 136 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11767 Z= 0.152 Angle : 0.555 11.039 16047 Z= 0.267 Chirality : 0.039 0.182 1847 Planarity : 0.004 0.069 1862 Dihedral : 9.830 127.341 2958 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.10 % Favored : 93.60 % Rotamer: Outliers : 1.96 % Allowed : 13.32 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.47 (0.24), residues: 1315 helix: -0.91 (0.21), residues: 673 sheet: -0.64 (0.41), residues: 162 loop : -0.90 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 PHE 0.018 0.001 PHE C 350 TYR 0.015 0.001 TYR A 598 ARG 0.004 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 198 ASP cc_start: 0.6837 (m-30) cc_final: 0.6600 (m-30) REVERT: C 276 MET cc_start: 0.6777 (mmp) cc_final: 0.6362 (tpt) REVERT: D 46 GLU cc_start: 0.7796 (pm20) cc_final: 0.6797 (mm-30) REVERT: D 166 MET cc_start: 0.8212 (mmt) cc_final: 0.7920 (mmm) REVERT: D 202 ASP cc_start: 0.8483 (t0) cc_final: 0.8129 (t70) REVERT: B 414 LYS cc_start: 0.6152 (tppt) cc_final: 0.4975 (tmtt) REVERT: B 596 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 620 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 538 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7148 (t80) REVERT: A 598 TYR cc_start: 0.8399 (t80) cc_final: 0.8192 (t80) REVERT: A 642 TRP cc_start: 0.7125 (m-10) cc_final: 0.6880 (m-90) REVERT: A 715 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7296 (mtp180) REVERT: A 716 ASP cc_start: 0.7825 (t0) cc_final: 0.7281 (m-30) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.2058 time to fit residues: 42.8344 Evaluate side-chains 141 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 114 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11767 Z= 0.133 Angle : 0.540 10.268 16047 Z= 0.261 Chirality : 0.039 0.184 1847 Planarity : 0.004 0.071 1862 Dihedral : 9.340 126.494 2958 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.41 % Favored : 94.28 % Rotamer: Outliers : 1.54 % Allowed : 14.35 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1315 helix: -0.65 (0.21), residues: 672 sheet: -0.57 (0.41), residues: 160 loop : -0.83 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.004 0.001 HIS B 652 PHE 0.017 0.001 PHE C 350 TYR 0.014 0.001 TYR A 598 ARG 0.003 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.242 Fit side-chains REVERT: C 190 ASP cc_start: 0.7718 (t0) cc_final: 0.7155 (m-30) REVERT: C 198 ASP cc_start: 0.6783 (m-30) cc_final: 0.6557 (m-30) REVERT: C 276 MET cc_start: 0.6744 (mmp) cc_final: 0.6375 (tpt) REVERT: C 363 TRP cc_start: 0.8245 (t60) cc_final: 0.8043 (t60) REVERT: D 46 GLU cc_start: 0.7796 (pm20) cc_final: 0.6771 (mm-30) REVERT: D 166 MET cc_start: 0.8228 (mmt) cc_final: 0.7947 (mmm) REVERT: D 202 ASP cc_start: 0.8441 (t0) cc_final: 0.8065 (t70) REVERT: B 414 LYS cc_start: 0.6184 (tppt) cc_final: 0.4990 (tmtt) REVERT: B 620 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6664 (tm-30) REVERT: A 525 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7366 (tpp80) REVERT: A 642 TRP cc_start: 0.7099 (m-10) cc_final: 0.6845 (m-90) REVERT: A 715 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7368 (mtp180) REVERT: A 716 ASP cc_start: 0.7859 (t0) cc_final: 0.7311 (m-30) outliers start: 18 outliers final: 16 residues processed: 151 average time/residue: 0.2308 time to fit residues: 50.7877 Evaluate side-chains 143 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11767 Z= 0.189 Angle : 0.582 11.744 16047 Z= 0.281 Chirality : 0.040 0.190 1847 Planarity : 0.004 0.070 1862 Dihedral : 9.381 125.960 2958 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.55 % Favored : 93.14 % Rotamer: Outliers : 1.62 % Allowed : 14.69 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.25 (0.24), residues: 1315 helix: -0.63 (0.21), residues: 671 sheet: -0.63 (0.41), residues: 162 loop : -0.94 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 180 HIS 0.004 0.001 HIS D 347 PHE 0.033 0.001 PHE B 423 TYR 0.016 0.001 TYR C 427 ARG 0.004 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.208 Fit side-chains REVERT: C 190 ASP cc_start: 0.7737 (t0) cc_final: 0.7140 (m-30) REVERT: C 198 ASP cc_start: 0.6829 (m-30) cc_final: 0.6587 (m-30) REVERT: C 276 MET cc_start: 0.6844 (mmp) cc_final: 0.6415 (tpt) REVERT: C 372 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7761 (mtt-85) REVERT: D 46 GLU cc_start: 0.7797 (pm20) cc_final: 0.6797 (mm-30) REVERT: D 166 MET cc_start: 0.8209 (mmt) cc_final: 0.7920 (mmm) REVERT: D 202 ASP cc_start: 0.8489 (t0) cc_final: 0.8110 (t70) REVERT: B 414 LYS cc_start: 0.6266 (tppt) cc_final: 0.5098 (tmtt) REVERT: B 453 ILE cc_start: 0.8296 (mt) cc_final: 0.8060 (tp) REVERT: B 620 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 525 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7369 (tpp80) REVERT: A 642 TRP cc_start: 0.7127 (m-10) cc_final: 0.6868 (m-90) REVERT: A 715 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7389 (mtp180) REVERT: A 716 ASP cc_start: 0.7867 (t0) cc_final: 0.7335 (m-30) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.2423 time to fit residues: 47.3722 Evaluate side-chains 139 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11767 Z= 0.163 Angle : 0.566 10.699 16047 Z= 0.274 Chirality : 0.040 0.192 1847 Planarity : 0.004 0.069 1862 Dihedral : 9.288 125.117 2958 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.02 % Favored : 93.67 % Rotamer: Outliers : 1.37 % Allowed : 15.12 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1315 helix: -0.57 (0.21), residues: 671 sheet: -0.58 (0.41), residues: 160 loop : -0.83 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 PHE 0.031 0.001 PHE B 423 TYR 0.014 0.001 TYR A 598 ARG 0.003 0.000 ARG C 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: C 190 ASP cc_start: 0.7754 (t0) cc_final: 0.7179 (m-30) REVERT: C 198 ASP cc_start: 0.6815 (m-30) cc_final: 0.6581 (m-30) REVERT: C 276 MET cc_start: 0.6881 (mmp) cc_final: 0.6444 (tpt) REVERT: C 372 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7730 (mtt-85) REVERT: D 46 GLU cc_start: 0.7796 (pm20) cc_final: 0.6801 (mm-30) REVERT: D 166 MET cc_start: 0.8206 (mmt) cc_final: 0.7916 (mmm) REVERT: D 202 ASP cc_start: 0.8477 (t0) cc_final: 0.8107 (t70) REVERT: D 226 MET cc_start: 0.8692 (mtp) cc_final: 0.8358 (mmm) REVERT: B 414 LYS cc_start: 0.6283 (tppt) cc_final: 0.5105 (tmtt) REVERT: B 620 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6680 (tm-30) REVERT: A 525 ARG cc_start: 0.7728 (mmt-90) cc_final: 0.7263 (tpp80) REVERT: A 642 TRP cc_start: 0.7113 (m-10) cc_final: 0.6852 (m-90) REVERT: A 716 ASP cc_start: 0.7909 (t0) cc_final: 0.7380 (m-30) outliers start: 16 outliers final: 16 residues processed: 132 average time/residue: 0.2337 time to fit residues: 44.2011 Evaluate side-chains 136 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain A residue 732 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126821 restraints weight = 22600.480| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.89 r_work: 0.2994 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11767 Z= 0.153 Angle : 0.559 11.294 16047 Z= 0.270 Chirality : 0.040 0.190 1847 Planarity : 0.004 0.067 1862 Dihedral : 9.156 124.490 2958 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.87 % Favored : 93.83 % Rotamer: Outliers : 1.79 % Allowed : 14.52 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1315 helix: -0.50 (0.21), residues: 672 sheet: -0.57 (0.41), residues: 160 loop : -0.84 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 65 HIS 0.003 0.001 HIS D 347 PHE 0.031 0.001 PHE B 423 TYR 0.015 0.001 TYR A 598 ARG 0.003 0.000 ARG C 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2657.70 seconds wall clock time: 48 minutes 41.52 seconds (2921.52 seconds total)