Starting phenix.real_space_refine on Mon Apr 8 20:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/04_2024/7fhl_31586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/04_2024/7fhl_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_31586/04_2024/7fhl_31586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/04_2024/7fhl_31586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/04_2024/7fhl_31586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhl_31586/04_2024/7fhl_31586.pdb" } resolution = 3.1 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= 0.000 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 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. 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-5288/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: 5.79, per 1000 atoms: 0.52 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: 4.46 Conformation dependent library (CDL) restraints added in 2.0 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: 1.07 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: 3.27 Time building geometry restraints manager: 4.81 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 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 % Allowed : 0.08 % Favored : 99.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS A 134 PHE 0.016 0.001 PHE C 426 TYR 0.018 0.001 TYR C 434 ARG 0.004 0.000 ARG C 324 *********************** 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 : 1.204 Fit side-chains REVERT: A 146 ILE cc_start: 0.8886 (mp) cc_final: 0.8550 (mm) REVERT: A 166 ASP cc_start: 0.9032 (t70) cc_final: 0.8795 (t0) REVERT: A 294 TYR cc_start: 0.8296 (m-10) cc_final: 0.7625 (m-10) REVERT: A 322 MET cc_start: 0.8782 (tmm) cc_final: 0.8554 (tmm) REVERT: A 393 GLN cc_start: 0.8548 (mm110) cc_final: 0.7764 (tm-30) REVERT: A 434 TYR cc_start: 0.8349 (m-80) cc_final: 0.7969 (m-80) REVERT: A 486 TYR cc_start: 0.8701 (m-80) cc_final: 0.8431 (m-10) REVERT: A 597 LYS cc_start: 0.8649 (tptm) cc_final: 0.8404 (tppt) REVERT: A 602 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 664 LEU cc_start: 0.8786 (mm) cc_final: 0.8156 (mm) REVERT: C 98 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7736 (mppt) REVERT: C 146 ILE cc_start: 0.8922 (mp) cc_final: 0.8595 (mm) REVERT: C 166 ASP cc_start: 0.9036 (t70) cc_final: 0.8780 (t0) REVERT: C 294 TYR cc_start: 0.8326 (m-10) cc_final: 0.7911 (m-10) REVERT: C 434 TYR cc_start: 0.8207 (m-80) cc_final: 0.7819 (m-80) REVERT: C 597 LYS cc_start: 0.8750 (tptt) cc_final: 0.8482 (tppt) REVERT: C 637 GLU cc_start: 0.7785 (pt0) cc_final: 0.6790 (pt0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2053 time to fit residues: 56.8201 Evaluate side-chains 153 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11350 Z= 0.307 Angle : 0.583 7.672 15440 Z= 0.308 Chirality : 0.039 0.172 1748 Planarity : 0.004 0.032 1914 Dihedral : 3.846 18.889 1468 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.68 % Allowed : 7.24 % Favored : 91.08 % 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: 1.85 (0.24), residues: 1318 helix: 1.59 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.009 0.002 HIS A 416 PHE 0.030 0.002 PHE C 408 TYR 0.023 0.002 TYR C 78 ARG 0.004 0.001 ARG A 279 *********************** 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 182 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.236 Fit side-chains REVERT: A 146 ILE cc_start: 0.8963 (mp) cc_final: 0.8622 (mm) REVERT: A 166 ASP cc_start: 0.9076 (t70) cc_final: 0.8799 (t0) REVERT: A 294 TYR cc_start: 0.8635 (m-10) cc_final: 0.8048 (m-10) REVERT: A 322 MET cc_start: 0.8810 (tmm) cc_final: 0.8504 (tmm) REVERT: A 393 GLN cc_start: 0.8378 (mm110) cc_final: 0.7671 (tm-30) REVERT: A 434 TYR cc_start: 0.8395 (m-80) cc_final: 0.8048 (m-80) REVERT: A 597 LYS cc_start: 0.8545 (tptm) cc_final: 0.8285 (tppt) REVERT: A 602 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 146 ILE cc_start: 0.8979 (mp) cc_final: 0.8656 (mm) REVERT: C 166 ASP cc_start: 0.9086 (t70) cc_final: 0.8797 (t0) REVERT: C 434 TYR cc_start: 0.8313 (m-80) cc_final: 0.8011 (m-80) REVERT: C 539 LEU cc_start: 0.8674 (mm) cc_final: 0.8374 (mm) REVERT: C 637 GLU cc_start: 0.7668 (pt0) cc_final: 0.7422 (pt0) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.1964 time to fit residues: 50.5126 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 526 ASN Chi-restraints excluded: chain C residue 542 ILE 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: 0.9990 chunk 101 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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: 0.8029 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11350 Z= 0.184 Angle : 0.511 7.748 15440 Z= 0.269 Chirality : 0.037 0.197 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.763 20.096 1468 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 8.84 % Favored : 89.39 % 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: 2.23 (0.24), residues: 1318 helix: 1.87 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.13 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 271 HIS 0.005 0.001 HIS A 416 PHE 0.026 0.001 PHE C 408 TYR 0.013 0.001 TYR C 78 ARG 0.002 0.000 ARG C 324 *********************** 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 182 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.111 Fit side-chains REVERT: A 86 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 166 ASP cc_start: 0.9028 (t70) cc_final: 0.8775 (t0) REVERT: A 294 TYR cc_start: 0.8607 (m-10) cc_final: 0.8056 (m-10) REVERT: A 322 MET cc_start: 0.8771 (tmm) cc_final: 0.8452 (tmm) REVERT: A 393 GLN cc_start: 0.8313 (mm110) cc_final: 0.7664 (tm-30) REVERT: A 434 TYR cc_start: 0.8348 (m-80) cc_final: 0.7997 (m-80) REVERT: A 602 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 146 ILE cc_start: 0.9002 (mp) cc_final: 0.8633 (mm) REVERT: C 166 ASP cc_start: 0.9053 (t70) cc_final: 0.8776 (t0) REVERT: C 294 TYR cc_start: 0.8527 (m-10) cc_final: 0.8091 (m-10) REVERT: C 408 PHE cc_start: 0.8166 (t80) cc_final: 0.7763 (t80) REVERT: C 434 TYR cc_start: 0.8240 (m-80) cc_final: 0.7911 (m-80) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.2048 time to fit residues: 52.8146 Evaluate side-chains 162 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.0010 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 81 optimal weight: 0.0270 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- 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 54 GLN ** C 416 HIS ** 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: 0.8005 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11350 Z= 0.157 Angle : 0.506 7.486 15440 Z= 0.265 Chirality : 0.037 0.197 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.703 19.620 1468 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.85 % Allowed : 10.19 % Favored : 87.96 % 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: 2.35 (0.24), residues: 1318 helix: 1.98 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 505 HIS 0.006 0.001 HIS C 416 PHE 0.030 0.001 PHE A 408 TYR 0.013 0.001 TYR A 305 ARG 0.006 0.000 ARG A 203 *********************** 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 180 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.214 Fit side-chains REVERT: A 98 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7850 (mppt) REVERT: A 166 ASP cc_start: 0.9009 (t70) cc_final: 0.8772 (t0) REVERT: A 294 TYR cc_start: 0.8571 (m-10) cc_final: 0.8015 (m-10) REVERT: A 322 MET cc_start: 0.8781 (tmm) cc_final: 0.8480 (tmm) REVERT: A 393 GLN cc_start: 0.8289 (mm110) cc_final: 0.7768 (tm-30) REVERT: A 434 TYR cc_start: 0.8369 (m-80) cc_final: 0.8047 (m-80) REVERT: A 602 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 98 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8126 (ptpt) REVERT: C 146 ILE cc_start: 0.9007 (mp) cc_final: 0.8616 (mm) REVERT: C 166 ASP cc_start: 0.9043 (t70) cc_final: 0.8763 (t0) REVERT: C 310 GLU cc_start: 0.8094 (tp30) cc_final: 0.7865 (tp30) REVERT: C 408 PHE cc_start: 0.8235 (t80) cc_final: 0.7985 (t80) REVERT: C 434 TYR cc_start: 0.8268 (m-80) cc_final: 0.7924 (m-80) outliers start: 22 outliers final: 11 residues processed: 169 average time/residue: 0.1961 time to fit residues: 49.6325 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 502 LEU 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: 2.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11350 Z= 0.255 Angle : 0.545 8.573 15440 Z= 0.284 Chirality : 0.038 0.195 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.709 20.216 1468 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 11.03 % Favored : 86.45 % 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: 1.91 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.16 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.007 0.001 HIS A 416 PHE 0.014 0.001 PHE A 501 TYR 0.013 0.002 TYR C 305 ARG 0.005 0.000 ARG A 200 *********************** 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 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.291 Fit side-chains REVERT: A 86 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 98 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7868 (mppt) REVERT: A 166 ASP cc_start: 0.9048 (t70) cc_final: 0.8767 (t0) REVERT: A 200 ARG cc_start: 0.6640 (tpp-160) cc_final: 0.6283 (tpp-160) REVERT: A 212 MET cc_start: 0.8764 (mmm) cc_final: 0.8349 (mtt) REVERT: A 322 MET cc_start: 0.8782 (tmm) cc_final: 0.8477 (tmm) REVERT: A 393 GLN cc_start: 0.8301 (mm110) cc_final: 0.7839 (tm-30) REVERT: A 434 TYR cc_start: 0.8351 (m-80) cc_final: 0.8048 (m-80) REVERT: A 602 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 86 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8018 (t80) REVERT: C 98 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8114 (ptpt) REVERT: C 166 ASP cc_start: 0.9064 (t70) cc_final: 0.8794 (t0) REVERT: C 310 GLU cc_start: 0.8195 (tp30) cc_final: 0.7901 (tp30) REVERT: C 408 PHE cc_start: 0.8253 (t80) cc_final: 0.7950 (t80) REVERT: C 434 TYR cc_start: 0.8282 (m-80) cc_final: 0.7945 (m-80) outliers start: 30 outliers final: 22 residues processed: 160 average time/residue: 0.2016 time to fit residues: 48.4685 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.0000 chunk 124 optimal weight: 4.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11350 Z= 0.159 Angle : 0.503 7.359 15440 Z= 0.263 Chirality : 0.037 0.200 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.666 19.759 1468 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 11.62 % Favored : 86.11 % 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: 2.36 (0.24), residues: 1318 helix: 1.99 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : 0.06 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 271 HIS 0.009 0.001 HIS A 416 PHE 0.033 0.001 PHE A 408 TYR 0.018 0.001 TYR A 491 ARG 0.002 0.000 ARG A 200 *********************** 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 179 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 98 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7881 (mppt) REVERT: A 166 ASP cc_start: 0.9003 (t70) cc_final: 0.8772 (t0) REVERT: A 212 MET cc_start: 0.8766 (mmm) cc_final: 0.8264 (mtt) REVERT: A 294 TYR cc_start: 0.8640 (m-10) cc_final: 0.8120 (m-10) REVERT: A 322 MET cc_start: 0.8762 (tmm) cc_final: 0.8469 (tmm) REVERT: A 393 GLN cc_start: 0.8287 (mm110) cc_final: 0.7852 (tm-30) REVERT: A 434 TYR cc_start: 0.8326 (m-80) cc_final: 0.8010 (m-80) REVERT: A 602 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 166 ASP cc_start: 0.9022 (t70) cc_final: 0.8774 (t0) REVERT: C 310 GLU cc_start: 0.8182 (tp30) cc_final: 0.7847 (tp30) REVERT: C 414 ILE cc_start: 0.8528 (mm) cc_final: 0.8233 (mm) REVERT: C 434 TYR cc_start: 0.8273 (m-80) cc_final: 0.7920 (m-80) outliers start: 27 outliers final: 20 residues processed: 166 average time/residue: 0.1980 time to fit residues: 49.2879 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR 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: 0.9990 chunk 72 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11350 Z= 0.172 Angle : 0.524 9.368 15440 Z= 0.270 Chirality : 0.037 0.213 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.604 18.905 1468 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.44 % Allowed : 12.71 % Favored : 84.85 % 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: 2.29 (0.24), residues: 1318 helix: 1.97 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.13 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 271 HIS 0.005 0.001 HIS A 416 PHE 0.014 0.001 PHE A 501 TYR 0.023 0.001 TYR A 491 ARG 0.002 0.000 ARG C 324 *********************** 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 180 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7914 (t80) REVERT: A 98 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7812 (mppt) REVERT: A 166 ASP cc_start: 0.9005 (t70) cc_final: 0.8774 (t0) REVERT: A 212 MET cc_start: 0.8753 (mmm) cc_final: 0.8213 (mtt) REVERT: A 294 TYR cc_start: 0.8661 (m-10) cc_final: 0.8134 (m-10) REVERT: A 320 ASP cc_start: 0.8806 (t70) cc_final: 0.8480 (t0) REVERT: A 322 MET cc_start: 0.8755 (tmm) cc_final: 0.8468 (tmm) REVERT: A 393 GLN cc_start: 0.8284 (mm110) cc_final: 0.7911 (tm-30) REVERT: A 434 TYR cc_start: 0.8313 (m-80) cc_final: 0.8022 (m-80) REVERT: A 602 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 86 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 98 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7898 (mppt) REVERT: C 166 ASP cc_start: 0.9019 (t70) cc_final: 0.8772 (t0) REVERT: C 434 TYR cc_start: 0.8273 (m-80) cc_final: 0.7906 (m-80) outliers start: 29 outliers final: 20 residues processed: 164 average time/residue: 0.1950 time to fit residues: 48.8435 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11350 Z= 0.170 Angle : 0.519 7.227 15440 Z= 0.271 Chirality : 0.038 0.213 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.610 18.242 1468 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 13.47 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.24), residues: 1318 helix: 1.99 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 271 HIS 0.004 0.001 HIS C 416 PHE 0.015 0.001 PHE A 501 TYR 0.016 0.001 TYR A 491 ARG 0.002 0.000 ARG C 324 *********************** 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 168 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 98 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7799 (mppt) REVERT: A 166 ASP cc_start: 0.9047 (t70) cc_final: 0.8841 (t0) REVERT: A 212 MET cc_start: 0.8790 (mmm) cc_final: 0.8242 (mtt) REVERT: A 294 TYR cc_start: 0.8654 (m-10) cc_final: 0.8095 (m-10) REVERT: A 320 ASP cc_start: 0.8810 (t70) cc_final: 0.8476 (t0) REVERT: A 322 MET cc_start: 0.8762 (tmm) cc_final: 0.8514 (tmm) REVERT: A 393 GLN cc_start: 0.8267 (mm110) cc_final: 0.7910 (tm-30) REVERT: A 434 TYR cc_start: 0.8300 (m-80) cc_final: 0.7991 (m-80) REVERT: C 86 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 98 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8028 (mptt) REVERT: C 166 ASP cc_start: 0.9020 (t70) cc_final: 0.8774 (t0) REVERT: C 434 TYR cc_start: 0.8279 (m-80) cc_final: 0.7908 (m-80) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.1958 time to fit residues: 46.3770 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 0.0070 chunk 127 optimal weight: 0.6980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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: 0.8000 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 : 0.003 0.067 11350 Z= 0.176 Angle : 0.534 9.078 15440 Z= 0.274 Chirality : 0.038 0.235 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.596 17.834 1468 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.27 % Allowed : 13.30 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.24), residues: 1318 helix: 2.06 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 271 HIS 0.004 0.001 HIS C 416 PHE 0.015 0.001 PHE A 501 TYR 0.014 0.001 TYR A 491 ARG 0.002 0.000 ARG C 324 *********************** 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 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 1.137 Fit side-chains REVERT: A 86 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 98 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7790 (mppt) REVERT: A 166 ASP cc_start: 0.9051 (t70) cc_final: 0.8832 (t0) REVERT: A 212 MET cc_start: 0.8793 (mmm) cc_final: 0.8249 (mtt) REVERT: A 310 GLU cc_start: 0.8215 (tp30) cc_final: 0.8015 (tp30) REVERT: A 320 ASP cc_start: 0.8793 (t70) cc_final: 0.8466 (t0) REVERT: A 322 MET cc_start: 0.8765 (tmm) cc_final: 0.8522 (tmm) REVERT: A 326 MET cc_start: 0.8019 (tmm) cc_final: 0.7588 (tmm) REVERT: A 393 GLN cc_start: 0.8265 (mm110) cc_final: 0.7913 (tm-30) REVERT: A 434 TYR cc_start: 0.8258 (m-80) cc_final: 0.7955 (m-80) REVERT: A 492 TRP cc_start: 0.8726 (t-100) cc_final: 0.8505 (t-100) REVERT: C 86 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7742 (t80) REVERT: C 98 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (mptt) REVERT: C 166 ASP cc_start: 0.9016 (t70) cc_final: 0.8772 (t0) REVERT: C 434 TYR cc_start: 0.8252 (m-80) cc_final: 0.7881 (m-80) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.1927 time to fit residues: 46.8321 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR 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: 0.1980 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11350 Z= 0.179 Angle : 0.525 8.418 15440 Z= 0.271 Chirality : 0.038 0.233 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.598 17.478 1468 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 13.80 % Favored : 84.18 % 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: 2.36 (0.24), residues: 1318 helix: 2.06 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 271 HIS 0.007 0.001 HIS A 416 PHE 0.016 0.001 PHE A 426 TYR 0.013 0.001 TYR A 491 ARG 0.002 0.000 ARG A 203 ********************** 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 165 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.351 Fit side-chains REVERT: A 86 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7948 (t80) REVERT: A 98 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: A 166 ASP cc_start: 0.9051 (t70) cc_final: 0.8832 (t0) REVERT: A 212 MET cc_start: 0.8793 (mmm) cc_final: 0.8242 (mtt) REVERT: A 310 GLU cc_start: 0.8230 (tp30) cc_final: 0.8022 (tp30) REVERT: A 320 ASP cc_start: 0.8795 (t70) cc_final: 0.8475 (t0) REVERT: A 322 MET cc_start: 0.8758 (tmm) cc_final: 0.8525 (tmm) REVERT: A 326 MET cc_start: 0.8011 (tmm) cc_final: 0.7431 (tmm) REVERT: A 393 GLN cc_start: 0.8260 (mm110) cc_final: 0.7917 (tm-30) REVERT: A 434 TYR cc_start: 0.8255 (m-80) cc_final: 0.7960 (m-80) REVERT: A 492 TRP cc_start: 0.8733 (t-100) cc_final: 0.8528 (t-100) REVERT: C 86 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7741 (t80) REVERT: C 98 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (mptt) REVERT: C 166 ASP cc_start: 0.9024 (t70) cc_final: 0.8772 (t0) REVERT: C 212 MET cc_start: 0.9043 (mtp) cc_final: 0.8842 (mtm) REVERT: C 434 TYR cc_start: 0.8268 (m-80) cc_final: 0.7898 (m-80) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.1986 time to fit residues: 46.3674 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR 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: 0.8980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** 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 = 0.137181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089852 restraints weight = 19026.651| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.66 r_work: 0.3071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11350 Z= 0.187 Angle : 0.536 10.785 15440 Z= 0.273 Chirality : 0.038 0.228 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.587 17.161 1468 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 13.47 % Favored : 84.51 % 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: 2.28 (0.24), residues: 1318 helix: 2.03 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.007 0.001 HIS A 416 PHE 0.016 0.001 PHE A 426 TYR 0.020 0.001 TYR A 415 ARG 0.002 0.000 ARG A 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.61 seconds wall clock time: 42 minutes 38.73 seconds (2558.73 seconds total)