Starting phenix.real_space_refine on Fri Jul 19 23:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlm_33284/07_2024/7xlm_33284.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6090 2.51 5 N 1478 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 582": "NH1" <-> "NH2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 714": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4629 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4629 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.63 Number of scatterers: 9268 At special positions: 0 Unit cell: (105.439, 127.179, 100.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1648 8.00 N 1478 7.00 C 6090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 58.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.902A pdb=" N GLY A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.948A pdb=" N GLN A 97 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP A 98 " --> pdb=" O VAL A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.888A pdb=" N ILE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.615A pdb=" N TYR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 removed outlier: 3.550A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 239 removed outlier: 3.626A pdb=" N MET A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.516A pdb=" N THR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 305 through 324 Proline residue: A 317 - end of helix removed outlier: 4.261A pdb=" N HIS A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.683A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.604A pdb=" N LEU A 378 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 403 removed outlier: 3.726A pdb=" N ILE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.847A pdb=" N ILE A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.533A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 4.031A pdb=" N LEU A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 510 through 524 removed outlier: 3.554A pdb=" N ILE A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 547 removed outlier: 3.998A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.560A pdb=" N ILE A 609 " --> pdb=" O ASN A 605 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.736A pdb=" N ARG A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.722A pdb=" N THR A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.734A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.902A pdb=" N GLY B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.948A pdb=" N GLN B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 98 " --> pdb=" O VAL B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.888A pdb=" N ILE B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.617A pdb=" N TYR B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 removed outlier: 3.550A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 239 removed outlier: 3.626A pdb=" N MET B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 removed outlier: 4.517A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 305 through 324 Proline residue: B 317 - end of helix removed outlier: 4.260A pdb=" N HIS B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.682A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.604A pdb=" N LEU B 378 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.727A pdb=" N ILE B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 424 removed outlier: 3.848A pdb=" N ILE B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 426 No H-bonds generated for 'chain 'B' and resid 425 through 426' Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.533A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 4.031A pdb=" N LEU B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 471 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 510 through 524 removed outlier: 3.554A pdb=" N ILE B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 547 removed outlier: 3.998A pdb=" N VAL B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 603 Processing helix chain 'B' and resid 605 through 616 removed outlier: 3.560A pdb=" N ILE B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 616 " --> pdb=" O ALA B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.736A pdb=" N ARG B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 678 " --> pdb=" O TYR B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.722A pdb=" N THR B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.734A pdb=" N VAL B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 removed outlier: 3.719A pdb=" N SER A 552 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 581 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 649 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.720A pdb=" N SER B 552 " --> pdb=" O ARG B 582 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 581 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 649 " --> pdb=" O LEU B 682 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2419 1.33 - 1.45: 1627 1.45 - 1.57: 5342 1.57 - 1.69: 0 1.69 - 1.80: 74 Bond restraints: 9462 Sorted by residual: bond pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.22e+00 bond pdb=" N ILE B 360 " pdb=" CA ILE B 360 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.60e+00 bond pdb=" N HIS A 363 " pdb=" CA HIS A 363 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 bond pdb=" N THR B 366 " pdb=" CA THR B 366 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 7.02e+00 ... (remaining 9457 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.75: 180 105.75 - 112.83: 5127 112.83 - 119.91: 3540 119.91 - 126.99: 3886 126.99 - 134.07: 105 Bond angle restraints: 12838 Sorted by residual: angle pdb=" C GLU A 558 " pdb=" N GLU A 559 " pdb=" CA GLU A 559 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C GLU B 558 " pdb=" N GLU B 559 " pdb=" CA GLU B 559 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C SER B 508 " pdb=" N ARG B 509 " pdb=" CA ARG B 509 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER A 508 " pdb=" N ARG A 509 " pdb=" CA ARG A 509 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ALA A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta sigma weight residual 121.41 129.21 -7.80 1.96e+00 2.60e-01 1.58e+01 ... (remaining 12833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4818 16.94 - 33.89: 606 33.89 - 50.83: 150 50.83 - 67.77: 28 67.77 - 84.72: 6 Dihedral angle restraints: 5608 sinusoidal: 2150 harmonic: 3458 Sorted by residual: dihedral pdb=" CA TYR A 699 " pdb=" C TYR A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual -180.00 -132.39 -47.61 0 5.00e+00 4.00e-02 9.07e+01 dihedral pdb=" CA TYR B 699 " pdb=" C TYR B 699 " pdb=" N CYS B 700 " pdb=" CA CYS B 700 " ideal model delta harmonic sigma weight residual 180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CA GLY A 697 " pdb=" C GLY A 697 " pdb=" N GLU A 698 " pdb=" CA GLU A 698 " ideal model delta harmonic sigma weight residual -180.00 -137.68 -42.32 0 5.00e+00 4.00e-02 7.16e+01 ... (remaining 5605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 992 0.050 - 0.100: 435 0.100 - 0.151: 88 0.151 - 0.201: 29 0.201 - 0.251: 8 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CB VAL B 557 " pdb=" CA VAL B 557 " pdb=" CG1 VAL B 557 " pdb=" CG2 VAL B 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 557 " pdb=" CA VAL A 557 " pdb=" CG1 VAL A 557 " pdb=" CG2 VAL A 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL B 382 " pdb=" CA VAL B 382 " pdb=" CG1 VAL B 382 " pdb=" CG2 VAL B 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1549 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 585 " -0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO B 586 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 585 " -0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO A 586 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 501 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 502 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.047 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2714 2.81 - 3.33: 8340 3.33 - 3.85: 14387 3.85 - 4.38: 15392 4.38 - 4.90: 27152 Nonbonded interactions: 67985 Sorted by model distance: nonbonded pdb=" OG SER A 538 " pdb=" OH TYR B 589 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR A 589 " pdb=" OG SER B 538 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 508 " pdb=" OD2 ASP B 511 " model vdw 2.302 2.440 nonbonded pdb=" OG SER A 508 " pdb=" OD2 ASP A 511 " model vdw 2.303 2.440 nonbonded pdb=" O SER B 254 " pdb=" OG SER B 254 " model vdw 2.328 2.440 ... (remaining 67980 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 'B' } 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 group one per residue 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.060 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 9462 Z= 0.535 Angle : 1.094 10.847 12838 Z= 0.580 Chirality : 0.060 0.251 1552 Planarity : 0.009 0.091 1556 Dihedral : 15.994 84.719 3376 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.69 % Favored : 87.05 % Rotamer: Outliers : 0.97 % Allowed : 14.44 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.18), residues: 1174 helix: -2.87 (0.14), residues: 680 sheet: -3.02 (0.83), residues: 36 loop : -4.20 (0.23), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 505 HIS 0.003 0.001 HIS B 324 PHE 0.022 0.002 PHE A 658 TYR 0.022 0.003 TYR B 588 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.048 Fit side-chains REVERT: A 88 MET cc_start: 0.6574 (ttp) cc_final: 0.6137 (ttp) REVERT: A 131 LEU cc_start: 0.8875 (tp) cc_final: 0.8595 (tt) REVERT: A 384 VAL cc_start: 0.8566 (t) cc_final: 0.8250 (p) REVERT: A 389 ILE cc_start: 0.9278 (pt) cc_final: 0.9073 (pt) REVERT: A 431 PHE cc_start: 0.7892 (m-80) cc_final: 0.7630 (m-80) REVERT: A 543 ILE cc_start: 0.9406 (pt) cc_final: 0.9095 (mt) REVERT: A 544 LEU cc_start: 0.9340 (tp) cc_final: 0.8661 (tt) REVERT: A 682 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 88 MET cc_start: 0.6576 (ttp) cc_final: 0.6134 (ttp) REVERT: B 131 LEU cc_start: 0.8851 (tp) cc_final: 0.8570 (tt) REVERT: B 384 VAL cc_start: 0.8562 (t) cc_final: 0.8245 (p) REVERT: B 389 ILE cc_start: 0.9276 (pt) cc_final: 0.9073 (pt) REVERT: B 431 PHE cc_start: 0.7872 (m-80) cc_final: 0.7627 (m-80) REVERT: B 543 ILE cc_start: 0.9408 (pt) cc_final: 0.9093 (mt) REVERT: B 544 LEU cc_start: 0.9339 (tp) cc_final: 0.8660 (tt) REVERT: B 682 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8774 (pp) outliers start: 10 outliers final: 4 residues processed: 166 average time/residue: 0.1873 time to fit residues: 44.6028 Evaluate side-chains 132 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 682 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 363 HIS ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 107 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 363 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9462 Z= 0.169 Angle : 0.643 8.162 12838 Z= 0.327 Chirality : 0.040 0.157 1552 Planarity : 0.005 0.060 1556 Dihedral : 6.107 39.820 1261 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.81 % Allowed : 19.67 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.23), residues: 1174 helix: -1.02 (0.19), residues: 680 sheet: -2.56 (0.92), residues: 36 loop : -3.77 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 505 HIS 0.011 0.001 HIS A 363 PHE 0.028 0.001 PHE A 152 TYR 0.012 0.001 TYR B 589 ARG 0.001 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.079 Fit side-chains REVERT: A 131 LEU cc_start: 0.8834 (tp) cc_final: 0.8580 (tt) REVERT: A 292 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7814 (m170) REVERT: A 384 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8132 (p) REVERT: A 543 ILE cc_start: 0.9307 (pt) cc_final: 0.9059 (mt) REVERT: A 544 LEU cc_start: 0.9309 (tp) cc_final: 0.8736 (tt) REVERT: A 682 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8531 (pp) REVERT: B 131 LEU cc_start: 0.8806 (tp) cc_final: 0.8559 (tt) REVERT: B 292 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7818 (m170) REVERT: B 384 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 543 ILE cc_start: 0.9308 (pt) cc_final: 0.9056 (mt) REVERT: B 544 LEU cc_start: 0.9314 (tp) cc_final: 0.8740 (tt) REVERT: B 682 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8526 (pp) outliers start: 29 outliers final: 8 residues processed: 171 average time/residue: 0.1524 time to fit residues: 40.3080 Evaluate side-chains 149 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 363 HIS ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9462 Z= 0.251 Angle : 0.653 7.682 12838 Z= 0.329 Chirality : 0.042 0.169 1552 Planarity : 0.004 0.053 1556 Dihedral : 5.729 40.214 1256 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.88 % Allowed : 22.38 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.48 (0.24), residues: 1174 helix: -0.31 (0.20), residues: 678 sheet: -2.58 (0.92), residues: 36 loop : -3.71 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 505 HIS 0.008 0.001 HIS B 292 PHE 0.033 0.002 PHE A 152 TYR 0.013 0.001 TYR A 589 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.132 Fit side-chains REVERT: A 131 LEU cc_start: 0.8845 (tp) cc_final: 0.8578 (tt) REVERT: A 384 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 543 ILE cc_start: 0.9343 (pt) cc_final: 0.9067 (mt) REVERT: A 544 LEU cc_start: 0.9339 (tp) cc_final: 0.8768 (tt) REVERT: A 682 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 131 LEU cc_start: 0.8816 (tp) cc_final: 0.8556 (tt) REVERT: B 384 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8194 (p) REVERT: B 543 ILE cc_start: 0.9335 (pt) cc_final: 0.9072 (mt) REVERT: B 544 LEU cc_start: 0.9348 (tp) cc_final: 0.8776 (tt) REVERT: B 682 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8603 (pp) outliers start: 40 outliers final: 28 residues processed: 163 average time/residue: 0.1508 time to fit residues: 38.1723 Evaluate side-chains 163 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 0.0070 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9462 Z= 0.167 Angle : 0.604 9.559 12838 Z= 0.301 Chirality : 0.040 0.165 1552 Planarity : 0.004 0.046 1556 Dihedral : 5.342 36.173 1256 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.17 % Allowed : 23.55 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.02 (0.24), residues: 1174 helix: 0.09 (0.20), residues: 690 sheet: -2.28 (0.97), residues: 36 loop : -3.68 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 505 HIS 0.001 0.000 HIS A 324 PHE 0.033 0.001 PHE B 152 TYR 0.010 0.001 TYR B 589 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.070 Fit side-chains REVERT: A 131 LEU cc_start: 0.8805 (tp) cc_final: 0.8534 (tt) REVERT: A 384 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 529 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 544 LEU cc_start: 0.9304 (tp) cc_final: 0.9018 (tt) REVERT: A 682 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8499 (pp) REVERT: B 131 LEU cc_start: 0.8768 (tp) cc_final: 0.8509 (tt) REVERT: B 384 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 529 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 544 LEU cc_start: 0.9324 (tp) cc_final: 0.9036 (tt) REVERT: B 682 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8491 (pp) outliers start: 43 outliers final: 28 residues processed: 169 average time/residue: 0.1601 time to fit residues: 42.1184 Evaluate side-chains 164 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9462 Z= 0.173 Angle : 0.602 10.271 12838 Z= 0.296 Chirality : 0.040 0.150 1552 Planarity : 0.003 0.043 1556 Dihedral : 5.162 35.834 1256 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.26 % Allowed : 24.52 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.71 (0.25), residues: 1174 helix: 0.38 (0.21), residues: 688 sheet: -2.16 (0.99), residues: 36 loop : -3.60 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.001 0.000 HIS A 292 PHE 0.033 0.001 PHE A 152 TYR 0.006 0.001 TYR B 588 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 0.992 Fit side-chains REVERT: A 131 LEU cc_start: 0.8760 (tp) cc_final: 0.8524 (tt) REVERT: A 376 TRP cc_start: 0.6301 (m-10) cc_final: 0.5792 (t60) REVERT: A 384 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 529 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 544 LEU cc_start: 0.9208 (tp) cc_final: 0.8941 (tt) REVERT: A 682 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8539 (pp) REVERT: B 131 LEU cc_start: 0.8723 (tp) cc_final: 0.8498 (tt) REVERT: B 349 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: B 376 TRP cc_start: 0.6311 (m-10) cc_final: 0.5800 (t60) REVERT: B 384 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 529 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 544 LEU cc_start: 0.9217 (tp) cc_final: 0.8957 (tt) REVERT: B 682 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8527 (pp) outliers start: 44 outliers final: 32 residues processed: 167 average time/residue: 0.1612 time to fit residues: 41.0902 Evaluate side-chains 169 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9462 Z= 0.228 Angle : 0.627 10.439 12838 Z= 0.309 Chirality : 0.041 0.189 1552 Planarity : 0.004 0.044 1556 Dihedral : 5.206 35.894 1256 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 5.04 % Allowed : 25.68 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.75 (0.25), residues: 1174 helix: 0.36 (0.21), residues: 700 sheet: -2.16 (0.99), residues: 36 loop : -3.76 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 505 HIS 0.002 0.001 HIS A 363 PHE 0.036 0.002 PHE A 152 TYR 0.010 0.001 TYR A 589 ARG 0.001 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 133 time to evaluate : 1.023 Fit side-chains REVERT: A 131 LEU cc_start: 0.8763 (tp) cc_final: 0.8513 (tt) REVERT: A 376 TRP cc_start: 0.6386 (m-10) cc_final: 0.5864 (t60) REVERT: A 384 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 529 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 544 LEU cc_start: 0.9231 (tp) cc_final: 0.8965 (tt) REVERT: A 682 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8583 (pp) REVERT: B 131 LEU cc_start: 0.8724 (tp) cc_final: 0.8485 (tt) REVERT: B 376 TRP cc_start: 0.6333 (m-10) cc_final: 0.5857 (t60) REVERT: B 384 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 529 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 544 LEU cc_start: 0.9237 (tp) cc_final: 0.8983 (tt) REVERT: B 682 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8577 (pp) outliers start: 52 outliers final: 39 residues processed: 170 average time/residue: 0.1599 time to fit residues: 41.0915 Evaluate side-chains 171 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9462 Z= 0.159 Angle : 0.602 10.807 12838 Z= 0.292 Chirality : 0.040 0.186 1552 Planarity : 0.003 0.042 1556 Dihedral : 4.998 33.702 1256 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.84 % Allowed : 25.87 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.54 (0.25), residues: 1174 helix: 0.52 (0.21), residues: 706 sheet: -2.12 (1.00), residues: 36 loop : -3.70 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.001 0.000 HIS A 292 PHE 0.036 0.001 PHE B 152 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.054 Fit side-chains REVERT: A 97 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6560 (tp40) REVERT: A 131 LEU cc_start: 0.8776 (tp) cc_final: 0.8512 (tt) REVERT: A 376 TRP cc_start: 0.6494 (m-10) cc_final: 0.5922 (t60) REVERT: A 384 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 529 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 544 LEU cc_start: 0.9199 (tp) cc_final: 0.8951 (tt) REVERT: A 682 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8480 (pp) REVERT: A 720 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 131 LEU cc_start: 0.8738 (tp) cc_final: 0.8482 (tt) REVERT: B 376 TRP cc_start: 0.6518 (m-10) cc_final: 0.5948 (t60) REVERT: B 384 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 529 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 544 LEU cc_start: 0.9202 (tp) cc_final: 0.8950 (tt) REVERT: B 682 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 720 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 50 outliers final: 36 residues processed: 176 average time/residue: 0.1514 time to fit residues: 41.3067 Evaluate side-chains 175 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9462 Z= 0.190 Angle : 0.619 12.982 12838 Z= 0.297 Chirality : 0.040 0.178 1552 Planarity : 0.003 0.040 1556 Dihedral : 4.979 33.885 1256 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 4.46 % Allowed : 26.26 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.48 (0.25), residues: 1174 helix: 0.59 (0.21), residues: 706 sheet: -2.12 (1.00), residues: 36 loop : -3.72 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 505 HIS 0.001 0.000 HIS B 665 PHE 0.035 0.001 PHE B 152 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 0.965 Fit side-chains REVERT: A 131 LEU cc_start: 0.8810 (tp) cc_final: 0.8566 (tt) REVERT: A 376 TRP cc_start: 0.6498 (m-10) cc_final: 0.5938 (t60) REVERT: A 384 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 529 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 544 LEU cc_start: 0.9226 (tp) cc_final: 0.8951 (tt) REVERT: A 682 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 131 LEU cc_start: 0.8769 (tp) cc_final: 0.8540 (tt) REVERT: B 376 TRP cc_start: 0.6503 (m-10) cc_final: 0.5944 (t60) REVERT: B 384 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 529 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 544 LEU cc_start: 0.9234 (tp) cc_final: 0.8960 (tt) REVERT: B 682 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8503 (pp) outliers start: 46 outliers final: 39 residues processed: 166 average time/residue: 0.1462 time to fit residues: 37.7869 Evaluate side-chains 174 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.002 0.022 9462 Z= 0.152 Angle : 0.622 13.193 12838 Z= 0.294 Chirality : 0.039 0.180 1552 Planarity : 0.003 0.040 1556 Dihedral : 4.891 32.838 1256 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.75 % Allowed : 26.16 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.39 (0.25), residues: 1174 helix: 0.68 (0.21), residues: 706 sheet: -2.05 (1.00), residues: 36 loop : -3.72 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.001 0.000 HIS A 292 PHE 0.036 0.001 PHE B 152 TYR 0.007 0.001 TYR B 589 ARG 0.001 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.120 Fit side-chains REVERT: A 97 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6437 (tp40) REVERT: A 376 TRP cc_start: 0.6510 (m-10) cc_final: 0.5856 (t60) REVERT: A 384 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 529 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 544 LEU cc_start: 0.9213 (tp) cc_final: 0.8946 (tt) REVERT: A 682 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8484 (pp) REVERT: A 720 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 376 TRP cc_start: 0.6513 (m-10) cc_final: 0.5860 (t60) REVERT: B 384 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 529 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8349 (mp) REVERT: B 544 LEU cc_start: 0.9216 (tp) cc_final: 0.8948 (tt) REVERT: B 682 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8471 (pp) REVERT: B 720 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 49 outliers final: 38 residues processed: 177 average time/residue: 0.1597 time to fit residues: 42.6707 Evaluate side-chains 182 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 0.0070 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9462 Z= 0.145 Angle : 0.623 13.154 12838 Z= 0.293 Chirality : 0.039 0.177 1552 Planarity : 0.003 0.039 1556 Dihedral : 4.828 32.492 1256 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.65 % Allowed : 26.45 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.33 (0.26), residues: 1174 helix: 0.74 (0.21), residues: 706 sheet: -1.98 (1.00), residues: 36 loop : -3.71 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.001 0.000 HIS A 292 PHE 0.036 0.001 PHE B 152 TYR 0.007 0.001 TYR B 589 ARG 0.001 0.000 ARG B 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.100 Fit side-chains REVERT: A 97 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6428 (tp40) REVERT: A 376 TRP cc_start: 0.6457 (m-10) cc_final: 0.5787 (t60) REVERT: A 384 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 529 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 544 LEU cc_start: 0.9207 (tp) cc_final: 0.8938 (tt) REVERT: A 682 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 720 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 376 TRP cc_start: 0.6462 (m-10) cc_final: 0.5782 (t60) REVERT: B 384 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 529 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8337 (mp) REVERT: B 544 LEU cc_start: 0.9211 (tp) cc_final: 0.8939 (tt) REVERT: B 682 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8457 (pp) REVERT: B 720 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7422 (tm-30) outliers start: 48 outliers final: 39 residues processed: 176 average time/residue: 0.1503 time to fit residues: 40.9170 Evaluate side-chains 185 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 0.0030 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN B 97 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.172588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147459 restraints weight = 13979.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150560 restraints weight = 8027.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152581 restraints weight = 5537.693| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9462 Z= 0.138 Angle : 0.634 13.161 12838 Z= 0.294 Chirality : 0.039 0.174 1552 Planarity : 0.003 0.038 1556 Dihedral : 4.765 32.037 1256 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.46 % Allowed : 27.13 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1174 helix: 0.80 (0.21), residues: 706 sheet: -1.96 (0.99), residues: 36 loop : -3.70 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 98 HIS 0.001 0.000 HIS A 292 PHE 0.035 0.001 PHE A 152 TYR 0.007 0.001 TYR B 142 ARG 0.001 0.000 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.19 seconds wall clock time: 32 minutes 44.71 seconds (1964.71 seconds total)