Starting phenix.real_space_refine (version: dev) on Tue Feb 21 08:55:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/02_2023/7fhl_31586.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3394 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 201": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.11, per 1000 atoms: 0.55 Number of scatterers: 11058 At special positions: 0 Unit cell: (88.218, 120.666, 117.624, 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) Ca 4 19.99 S 44 16.00 O 1954 8.00 N 1710 7.00 C 7346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " 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=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 87.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.582A pdb=" N LEU A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.790A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.700A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.763A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 239 removed outlier: 3.595A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.596A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.802A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.975A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.352A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.503A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 4.513A pdb=" N LYS A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.584A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.649A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.510A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.504A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 3.837A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.982A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 Processing helix chain 'A' and resid 528 through 538 removed outlier: 4.514A pdb=" N TYR A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.747A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.686A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 removed outlier: 3.535A pdb=" N GLN A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.700A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.656A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.823A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 659 removed outlier: 4.081A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.633A pdb=" N LEU C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 70 through 88 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.786A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.716A pdb=" N GLY C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.891A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 239 removed outlier: 4.478A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.826A pdb=" N THR C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.982A pdb=" N VAL C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 294 removed outlier: 4.152A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 335 removed outlier: 3.538A pdb=" N ALA C 330 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 4.552A pdb=" N LYS C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 357 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 376 Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.576A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 430 through 457 Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.997A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.979A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.586A pdb=" N PHE C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 removed outlier: 4.295A pdb=" N TYR C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 533 " --> pdb=" O TRP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 545 removed outlier: 4.022A pdb=" N ARG C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 539 through 545' Processing helix chain 'C' and resid 548 through 565 removed outlier: 4.636A pdb=" N ALA C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 removed outlier: 3.806A pdb=" N GLN C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.659A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.524A pdb=" N ASN C 612 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 628 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.617A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 4.151A pdb=" N THR C 650 " --> pdb=" O TRP C 646 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR C 651 " --> pdb=" O TRP C 647 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 Processing helix chain 'D' and resid 7 through 17 747 hydrogen bonds defined for protein. 2220 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: 3.12 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3361 1.34 - 1.46: 2992 1.46 - 1.58: 4925 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 11350 Sorted by residual: bond pdb=" C LYS C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.20e-02 6.94e+03 1.45e+00 bond pdb=" CA ILE A 562 " pdb=" CB ILE A 562 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.08e+00 bond pdb=" N THR A 517 " pdb=" CA THR A 517 " ideal model delta sigma weight residual 1.463 1.450 0.013 1.22e-02 6.72e+03 1.07e+00 bond pdb=" C LYS A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.20e-02 6.94e+03 9.72e-01 bond pdb=" C ILE C 272 " pdb=" N PRO C 273 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 9.25e-01 ... (remaining 11345 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.51: 118 104.51 - 111.91: 5483 111.91 - 119.31: 3641 119.31 - 126.71: 6027 126.71 - 134.11: 171 Bond angle restraints: 15440 Sorted by residual: angle pdb=" CB MET A 629 " pdb=" CG MET A 629 " pdb=" SD MET A 629 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.19e+00 angle pdb=" CA PRO A 97 " pdb=" C PRO A 97 " pdb=" N LYS A 98 " ideal model delta sigma weight residual 114.66 117.48 -2.82 1.34e+00 5.57e-01 4.42e+00 angle pdb=" C SER C 55 " pdb=" N SER C 56 " pdb=" CA SER C 56 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.41e+00 angle pdb=" C SER A 55 " pdb=" N SER A 56 " pdb=" CA SER A 56 " ideal model delta sigma weight residual 121.54 125.52 -3.98 1.91e+00 2.74e-01 4.34e+00 angle pdb=" CA PRO C 97 " pdb=" C PRO C 97 " pdb=" N LYS C 98 " ideal model delta sigma weight residual 114.66 117.44 -2.78 1.34e+00 5.57e-01 4.31e+00 ... (remaining 15435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6049 17.64 - 35.29: 434 35.29 - 52.93: 68 52.93 - 70.58: 15 70.58 - 88.22: 6 Dihedral angle restraints: 6572 sinusoidal: 2576 harmonic: 3996 Sorted by residual: dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 98 " pdb=" C LYS A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 65.17 27.83 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 6569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1196 0.029 - 0.058: 368 0.058 - 0.087: 131 0.087 - 0.116: 46 0.116 - 0.145: 7 Chirality restraints: 1748 Sorted by residual: chirality pdb=" CB ILE C 272 " pdb=" CA ILE C 272 " pdb=" CG1 ILE C 272 " pdb=" CG2 ILE C 272 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1745 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 308 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C PHE C 308 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE C 308 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS C 309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 314 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C LYS C 314 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS C 314 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN C 315 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 317 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C SER C 317 " 0.029 2.00e-02 2.50e+03 pdb=" O SER C 317 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY C 318 " -0.010 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 12186 3.25 - 3.80: 17414 3.80 - 4.35: 21599 4.35 - 4.90: 35706 Nonbonded interactions: 87047 Sorted by model distance: nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.150 2.440 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.151 2.440 nonbonded pdb=" O TYR C 107 " pdb=" ND2 ASN C 614 " model vdw 2.186 2.520 nonbonded pdb=" O TYR A 107 " pdb=" ND2 ASN A 614 " model vdw 2.196 2.520 nonbonded pdb=" O PHE C 426 " pdb=" OG SER C 429 " model vdw 2.222 2.440 ... (remaining 87042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 44 5.16 5 C 7346 2.51 5 N 1710 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.770 Check model and map are aligned: 0.160 Process input model: 30.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.002 0.035 11350 Z= 0.154 Angle : 0.548 7.463 15440 Z= 0.304 Chirality : 0.035 0.145 1748 Planarity : 0.004 0.030 1914 Dihedral : 12.500 88.221 3982 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1318 helix: 1.14 (0.16), residues: 970 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2041 time to fit residues: 56.6948 Evaluate side-chains 148 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN C 54 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 11350 Z= 0.363 Angle : 0.609 7.813 15440 Z= 0.322 Chirality : 0.040 0.168 1748 Planarity : 0.004 0.033 1914 Dihedral : 3.912 19.270 1468 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1318 helix: 1.49 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : 0.16 (0.41), residues: 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.262 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 162 average time/residue: 0.2011 time to fit residues: 49.1568 Evaluate side-chains 146 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0998 time to fit residues: 4.1624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 267 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11350 Z= 0.274 Angle : 0.563 7.719 15440 Z= 0.296 Chirality : 0.039 0.201 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.884 21.815 1468 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1318 helix: 1.70 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.266 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 152 average time/residue: 0.2112 time to fit residues: 48.1422 Evaluate side-chains 143 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1683 time to fit residues: 3.4668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 0.0470 chunk 81 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 11350 Z= 0.148 Angle : 0.503 7.519 15440 Z= 0.264 Chirality : 0.036 0.198 1748 Planarity : 0.003 0.034 1914 Dihedral : 3.721 19.963 1468 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1318 helix: 1.98 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.05 (0.40), residues: 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.274 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 175 average time/residue: 0.2016 time to fit residues: 52.8631 Evaluate side-chains 151 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 116 optimal weight: 0.4980 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 11350 Z= 0.325 Angle : 0.582 8.222 15440 Z= 0.303 Chirality : 0.040 0.191 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.756 16.572 1468 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1318 helix: 1.78 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.257 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 153 average time/residue: 0.2108 time to fit residues: 48.1227 Evaluate side-chains 145 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1034 time to fit residues: 4.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 11350 Z= 0.170 Angle : 0.509 7.454 15440 Z= 0.267 Chirality : 0.036 0.212 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.690 16.700 1468 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.24), residues: 1318 helix: 1.98 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.428 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 0.2050 time to fit residues: 46.5736 Evaluate side-chains 139 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1001 time to fit residues: 2.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11350 Z= 0.164 Angle : 0.514 9.054 15440 Z= 0.268 Chirality : 0.037 0.221 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.590 15.722 1468 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1318 helix: 2.02 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.377 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 146 average time/residue: 0.2108 time to fit residues: 46.5596 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1050 time to fit residues: 2.3036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 11350 Z= 0.307 Angle : 0.577 8.344 15440 Z= 0.301 Chirality : 0.039 0.208 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.690 17.524 1468 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1318 helix: 1.83 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -0.12 (0.41), residues: 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.207 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 141 average time/residue: 0.2088 time to fit residues: 44.5972 Evaluate side-chains 136 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1114 time to fit residues: 3.2224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 11350 Z= 0.173 Angle : 0.536 9.375 15440 Z= 0.278 Chirality : 0.037 0.221 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.639 17.484 1468 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1318 helix: 1.95 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.167 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 139 average time/residue: 0.1992 time to fit residues: 42.4043 Evaluate side-chains 131 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1086 time to fit residues: 2.5646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 11350 Z= 0.192 Angle : 0.547 12.151 15440 Z= 0.281 Chirality : 0.038 0.224 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.609 17.266 1468 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.24), residues: 1318 helix: 1.93 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.496 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 134 average time/residue: 0.2031 time to fit residues: 41.6017 Evaluate side-chains 133 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1097 time to fit residues: 2.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0030 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.137182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089842 restraints weight = 19176.581| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.65 r_work: 0.3073 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 11350 Z= 0.183 Angle : 0.555 11.998 15440 Z= 0.283 Chirality : 0.038 0.224 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.583 16.798 1468 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.24), residues: 1318 helix: 1.94 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 282 =============================================================================== Job complete usr+sys time: 2126.40 seconds wall clock time: 39 minutes 15.20 seconds (2355.20 seconds total)