Starting phenix.real_space_refine on Mon Mar 11 13:31:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa3_11689/03_2024/7aa3_11689.pdb" } resolution = 3.56 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= 0.031 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 29 5.16 5 C 5336 2.51 5 N 1438 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ASP 682": "OD1" <-> "OD2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "B ASP 735": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4211 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 29, 'TRANS': 520} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4178 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.83, per 1000 atoms: 0.58 Number of scatterers: 8389 At special positions: 0 Unit cell: (101.85, 122.85, 81.9, 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 29 16.00 O 1586 8.00 N 1438 7.00 C 5336 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 48.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.771A pdb=" N THR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.527A pdb=" N HIS A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.595A pdb=" N ILE A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.115A pdb=" N ARG A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 148 through 156 removed outlier: 5.028A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.535A pdb=" N MET A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.539A pdb=" N VAL A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.132A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 removed outlier: 3.517A pdb=" N GLU A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.895A pdb=" N ASP A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.667A pdb=" N ALA A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.560A pdb=" N SER A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.940A pdb=" N LEU A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.124A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.593A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 3.791A pdb=" N LYS A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 4.435A pdb=" N LEU A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.710A pdb=" N GLY A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.675A pdb=" N GLN A 578 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 617 removed outlier: 3.799A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 663 removed outlier: 4.020A pdb=" N LEU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 4.052A pdb=" N TYR A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 removed outlier: 3.575A pdb=" N PHE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.817A pdb=" N PHE A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 738' Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.512A pdb=" N MET B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.623A pdb=" N PHE B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.900A pdb=" N LYS B 158 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 159 " --> pdb=" O GLY B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.787A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.713A pdb=" N ARG B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 4.311A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 413 removed outlier: 4.054A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.989A pdb=" N LEU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 removed outlier: 4.078A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.580A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.508A pdb=" N VAL B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 560 removed outlier: 3.981A pdb=" N LEU B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 635 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.592A pdb=" N LEU B 641 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.741A pdb=" N ALA B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 removed outlier: 3.579A pdb=" N PHE B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 667 through 670 removed outlier: 6.870A pdb=" N GLY A 680 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 667 through 668 253 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 3.19 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: 2807 1.34 - 1.46: 1865 1.46 - 1.58: 3863 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8589 Sorted by residual: bond pdb=" CB VAL B 166 " pdb=" CG1 VAL B 166 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.61e+00 bond pdb=" CA ARG B 104 " pdb=" C ARG B 104 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.72e-02 3.38e+03 2.49e+00 bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.57e+00 bond pdb=" CB ILE B 416 " pdb=" CG2 ILE B 416 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" C ASN A 238 " pdb=" N PRO A 239 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 ... (remaining 8584 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 223 105.94 - 112.96: 4530 112.96 - 119.99: 3091 119.99 - 127.02: 3710 127.02 - 134.04: 135 Bond angle restraints: 11689 Sorted by residual: angle pdb=" N LEU A 382 " pdb=" CA LEU A 382 " pdb=" C LEU A 382 " ideal model delta sigma weight residual 113.72 108.77 4.95 1.52e+00 4.33e-01 1.06e+01 angle pdb=" CB LYS A 433 " pdb=" CG LYS A 433 " pdb=" CD LYS A 433 " ideal model delta sigma weight residual 111.30 118.21 -6.91 2.30e+00 1.89e-01 9.03e+00 angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 106.21 109.13 -2.92 1.07e+00 8.73e-01 7.42e+00 angle pdb=" C PRO A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 121.65 119.13 2.52 9.40e-01 1.13e+00 7.18e+00 angle pdb=" N VAL A 267 " pdb=" CA VAL A 267 " pdb=" C VAL A 267 " ideal model delta sigma weight residual 109.34 104.26 5.08 2.08e+00 2.31e-01 5.96e+00 ... (remaining 11684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4515 17.74 - 35.49: 424 35.49 - 53.23: 73 53.23 - 70.98: 9 70.98 - 88.72: 8 Dihedral angle restraints: 5029 sinusoidal: 1925 harmonic: 3104 Sorted by residual: dihedral pdb=" CA HIS B 97 " pdb=" C HIS B 97 " pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP B 406 " pdb=" C ASP B 406 " pdb=" N GLU B 407 " pdb=" CA GLU B 407 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA VAL A 423 " pdb=" C VAL A 423 " pdb=" N ALA A 424 " pdb=" CA ALA A 424 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 658 0.030 - 0.059: 422 0.059 - 0.089: 136 0.089 - 0.118: 54 0.118 - 0.147: 7 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA VAL A 267 " pdb=" N VAL A 267 " pdb=" C VAL A 267 " pdb=" CB VAL A 267 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB VAL B 151 " pdb=" CA VAL B 151 " pdb=" CG1 VAL B 151 " pdb=" CG2 VAL B 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CB ILE B 416 " pdb=" CA ILE B 416 " pdb=" CG1 ILE B 416 " pdb=" CG2 ILE B 416 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1274 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 99 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 100 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 149 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 150 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 149 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 150 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.021 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 103 2.62 - 3.19: 7649 3.19 - 3.76: 11793 3.76 - 4.33: 16797 4.33 - 4.90: 27958 Nonbonded interactions: 64300 Sorted by model distance: nonbonded pdb=" OH TYR B 337 " pdb=" O THR B 394 " model vdw 2.046 2.440 nonbonded pdb=" O TRP A 91 " pdb=" OH TYR A 98 " model vdw 2.155 2.440 nonbonded pdb=" OG SER B 539 " pdb=" O ARG B 571 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR A 113 " pdb=" OD2 ASP A 487 " model vdw 2.209 2.440 nonbonded pdb=" OD2 ASP A 79 " pdb=" NZ LYS A 154 " model vdw 2.227 2.520 ... (remaining 64295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 124 or resid 141 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) \ or resid 191 through 193 or resid 242 through 341 or (resid 342 through 379 and \ (name N or name CA or name C or name O or name CB )) or resid 380 through 432 o \ r (resid 433 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 34 through 680 or (resid 681 and (name N or name CA or name C or name O or name \ CB )) or resid 682 through 739)) selection = (chain 'B' and (resid 43 through 271 or (resid 272 and (name N or name CA or nam \ e C or name O or name CB )) or resid 329 through 343 or resid 379 through 391 or \ (resid 392 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 3 through 502 or (resid 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 through 514 or (resid 515 through 516 and (name N or name CA o \ r name C or name O or name CB )) or resid 517 through 687 or (resid 688 and (nam \ e N or name CA or name C or name O or name CB )) or resid 689 through 736 or (re \ sid 737 and (name N or name CA or name C or name O or name CB )) or resid 738 th \ rough 739)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.990 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: 0.000 Extract box with map and model: 5.500 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.240 Find NCS groups from input model: 0.510 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.004 0.053 8589 Z= 0.289 Angle : 0.659 7.285 11689 Z= 0.365 Chirality : 0.043 0.147 1277 Planarity : 0.004 0.052 1533 Dihedral : 14.112 88.722 3039 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -3.38 (0.24), residues: 1074 helix: -1.92 (0.24), residues: 454 sheet: -4.27 (0.99), residues: 20 loop : -2.49 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.003 0.001 HIS B 561 PHE 0.012 0.001 PHE A 332 TYR 0.010 0.001 TYR A 638 ARG 0.006 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8144 (t60) cc_final: 0.7710 (t-100) REVERT: A 535 ASN cc_start: 0.8543 (t0) cc_final: 0.8251 (t0) REVERT: A 664 MET cc_start: 0.8612 (mmm) cc_final: 0.8306 (tpp) REVERT: B 416 ILE cc_start: 0.8497 (mm) cc_final: 0.8217 (mt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1933 time to fit residues: 20.6065 Evaluate side-chains 59 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8589 Z= 0.204 Angle : 0.575 6.929 11689 Z= 0.291 Chirality : 0.040 0.140 1277 Planarity : 0.004 0.048 1533 Dihedral : 5.237 23.903 1174 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.24 % Allowed : 7.89 % Favored : 91.87 % 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: -2.86 (0.25), residues: 1074 helix: -1.56 (0.25), residues: 464 sheet: -4.20 (0.97), residues: 20 loop : -2.11 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.002 0.001 HIS B 116 PHE 0.010 0.001 PHE A 332 TYR 0.016 0.001 TYR A 638 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.980 Fit side-chains REVERT: A 58 MET cc_start: 0.7828 (mmt) cc_final: 0.7578 (mmm) REVERT: A 107 TRP cc_start: 0.8371 (t60) cc_final: 0.7803 (t-100) REVERT: A 535 ASN cc_start: 0.8562 (t0) cc_final: 0.8285 (t0) REVERT: B 416 ILE cc_start: 0.8494 (mm) cc_final: 0.8204 (mt) REVERT: B 562 ASN cc_start: 0.8278 (p0) cc_final: 0.7950 (t0) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.1995 time to fit residues: 21.4222 Evaluate side-chains 64 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.0040 overall best weight: 0.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8589 Z= 0.129 Angle : 0.520 7.423 11689 Z= 0.261 Chirality : 0.038 0.134 1277 Planarity : 0.004 0.039 1533 Dihedral : 4.641 22.749 1174 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.71 % Allowed : 10.25 % Favored : 89.05 % 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: -2.45 (0.25), residues: 1074 helix: -1.12 (0.25), residues: 455 sheet: -4.18 (0.88), residues: 20 loop : -1.97 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.002 0.001 HIS B 116 PHE 0.006 0.001 PHE B 657 TYR 0.015 0.001 TYR B 638 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8394 (t60) cc_final: 0.8154 (t60) REVERT: A 145 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7859 (ttp-170) REVERT: A 535 ASN cc_start: 0.8529 (t0) cc_final: 0.8325 (t0) REVERT: B 416 ILE cc_start: 0.8405 (mm) cc_final: 0.8103 (mt) REVERT: B 735 ASP cc_start: 0.8445 (t0) cc_final: 0.8225 (t0) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.1729 time to fit residues: 20.5602 Evaluate side-chains 67 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8589 Z= 0.212 Angle : 0.537 6.842 11689 Z= 0.270 Chirality : 0.040 0.121 1277 Planarity : 0.003 0.038 1533 Dihedral : 4.662 23.825 1174 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.41 % Allowed : 11.78 % Favored : 86.81 % 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: -2.42 (0.25), residues: 1074 helix: -1.10 (0.25), residues: 463 sheet: -4.14 (0.91), residues: 20 loop : -1.95 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.013 0.001 PHE A 332 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8347 (t60) cc_final: 0.8117 (t60) REVERT: A 145 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7718 (ttp-170) REVERT: A 535 ASN cc_start: 0.8602 (t0) cc_final: 0.8246 (t0) REVERT: A 608 TYR cc_start: 0.8406 (m-80) cc_final: 0.8069 (m-80) REVERT: B 416 ILE cc_start: 0.8473 (mm) cc_final: 0.8156 (mt) REVERT: B 668 TRP cc_start: 0.8496 (m100) cc_final: 0.8169 (m100) REVERT: B 735 ASP cc_start: 0.8520 (t0) cc_final: 0.8314 (t0) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.1749 time to fit residues: 21.0435 Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 508 ASN B 602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8589 Z= 0.164 Angle : 0.519 7.717 11689 Z= 0.261 Chirality : 0.039 0.122 1277 Planarity : 0.003 0.036 1533 Dihedral : 4.524 23.542 1174 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.18 % Allowed : 13.31 % Favored : 85.51 % 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: -2.29 (0.25), residues: 1074 helix: -0.94 (0.25), residues: 459 sheet: -4.23 (0.91), residues: 20 loop : -1.92 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.009 0.001 PHE A 332 TYR 0.006 0.001 TYR B 98 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7705 (ttp-170) REVERT: A 535 ASN cc_start: 0.8603 (t0) cc_final: 0.8266 (t0) REVERT: A 608 TYR cc_start: 0.8404 (m-80) cc_final: 0.8030 (m-80) REVERT: B 416 ILE cc_start: 0.8437 (mm) cc_final: 0.8121 (mt) REVERT: B 668 TRP cc_start: 0.8495 (m100) cc_final: 0.8180 (m100) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.2655 time to fit residues: 33.0329 Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 0.0570 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8589 Z= 0.158 Angle : 0.532 8.627 11689 Z= 0.266 Chirality : 0.039 0.149 1277 Planarity : 0.003 0.035 1533 Dihedral : 4.379 23.822 1174 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.41 % Allowed : 14.84 % Favored : 83.75 % 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: -2.15 (0.25), residues: 1074 helix: -0.79 (0.25), residues: 460 sheet: -4.23 (0.89), residues: 20 loop : -1.87 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.009 0.001 PHE A 332 TYR 0.017 0.001 TYR B 638 ARG 0.006 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7676 (ttp-170) REVERT: A 535 ASN cc_start: 0.8559 (t0) cc_final: 0.8301 (t0) REVERT: A 608 TYR cc_start: 0.8382 (m-80) cc_final: 0.8003 (m-80) REVERT: B 416 ILE cc_start: 0.8407 (mm) cc_final: 0.8089 (mt) REVERT: B 668 TRP cc_start: 0.8482 (m100) cc_final: 0.8113 (m100) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.1834 time to fit residues: 21.0280 Evaluate side-chains 76 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8589 Z= 0.156 Angle : 0.522 10.332 11689 Z= 0.260 Chirality : 0.039 0.120 1277 Planarity : 0.003 0.035 1533 Dihedral : 4.303 24.708 1174 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.65 % Allowed : 15.08 % Favored : 83.27 % 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: -2.08 (0.25), residues: 1074 helix: -0.73 (0.25), residues: 466 sheet: -4.13 (0.90), residues: 20 loop : -1.85 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.000 HIS B 116 PHE 0.010 0.001 PHE A 332 TYR 0.005 0.001 TYR B 98 ARG 0.001 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7675 (ttp-170) REVERT: A 535 ASN cc_start: 0.8563 (t0) cc_final: 0.8321 (t0) REVERT: A 608 TYR cc_start: 0.8377 (m-80) cc_final: 0.8000 (m-80) REVERT: B 105 MET cc_start: 0.7927 (ttp) cc_final: 0.7665 (ttp) REVERT: B 416 ILE cc_start: 0.8398 (mm) cc_final: 0.8076 (mt) REVERT: B 668 TRP cc_start: 0.8473 (m100) cc_final: 0.8189 (m100) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1617 time to fit residues: 19.4654 Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0070 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8589 Z= 0.151 Angle : 0.527 11.215 11689 Z= 0.261 Chirality : 0.039 0.121 1277 Planarity : 0.003 0.037 1533 Dihedral : 4.237 23.862 1174 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.88 % Allowed : 15.43 % Favored : 82.69 % 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: -1.97 (0.25), residues: 1074 helix: -0.62 (0.25), residues: 466 sheet: -4.01 (0.91), residues: 20 loop : -1.80 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.008 0.001 PHE A 332 TYR 0.022 0.001 TYR B 638 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7683 (ttp-170) REVERT: A 608 TYR cc_start: 0.8389 (m-80) cc_final: 0.8008 (m-80) REVERT: B 416 ILE cc_start: 0.8383 (mm) cc_final: 0.8064 (mt) REVERT: B 623 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: B 668 TRP cc_start: 0.8466 (m100) cc_final: 0.8168 (m100) outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1718 time to fit residues: 20.3929 Evaluate side-chains 80 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8589 Z= 0.288 Angle : 0.599 10.071 11689 Z= 0.300 Chirality : 0.042 0.126 1277 Planarity : 0.004 0.036 1533 Dihedral : 4.640 23.927 1174 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.65 % Allowed : 16.14 % Favored : 82.21 % 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: -2.16 (0.25), residues: 1074 helix: -0.83 (0.25), residues: 469 sheet: -3.97 (0.93), residues: 20 loop : -1.87 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS B 116 PHE 0.016 0.001 PHE A 332 TYR 0.025 0.001 TYR B 638 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.963 Fit side-chains REVERT: A 419 ASP cc_start: 0.7929 (t0) cc_final: 0.7630 (t0) REVERT: A 608 TYR cc_start: 0.8438 (m-80) cc_final: 0.8066 (m-80) REVERT: B 416 ILE cc_start: 0.8497 (mm) cc_final: 0.8188 (mt) REVERT: B 623 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: B 668 TRP cc_start: 0.8500 (m100) cc_final: 0.8277 (m100) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.1582 time to fit residues: 18.8501 Evaluate side-chains 74 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 68 optimal weight: 0.0040 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8589 Z= 0.146 Angle : 0.546 11.630 11689 Z= 0.270 Chirality : 0.038 0.123 1277 Planarity : 0.003 0.036 1533 Dihedral : 4.268 23.734 1174 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.18 % Allowed : 17.31 % Favored : 81.51 % 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: -1.86 (0.26), residues: 1074 helix: -0.55 (0.25), residues: 468 sheet: -3.91 (0.92), residues: 20 loop : -1.73 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.003 0.000 HIS B 116 PHE 0.006 0.001 PHE A 657 TYR 0.023 0.001 TYR B 638 ARG 0.002 0.000 ARG A 571 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.952 Fit side-chains REVERT: A 145 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7840 (ttp-170) REVERT: A 419 ASP cc_start: 0.7828 (t0) cc_final: 0.7559 (t0) REVERT: A 608 TYR cc_start: 0.8397 (m-80) cc_final: 0.7984 (m-80) REVERT: B 416 ILE cc_start: 0.8409 (mm) cc_final: 0.8094 (mt) REVERT: B 419 ASP cc_start: 0.7905 (p0) cc_final: 0.7636 (p0) REVERT: B 623 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: B 668 TRP cc_start: 0.8451 (m100) cc_final: 0.8164 (m100) REVERT: B 735 ASP cc_start: 0.8459 (t0) cc_final: 0.8257 (t0) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.1771 time to fit residues: 19.6831 Evaluate side-chains 73 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103641 restraints weight = 13581.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107777 restraints weight = 7807.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110651 restraints weight = 5398.067| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8589 Z= 0.187 Angle : 0.563 11.346 11689 Z= 0.276 Chirality : 0.039 0.123 1277 Planarity : 0.003 0.035 1533 Dihedral : 4.296 23.380 1174 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.65 % Allowed : 16.61 % Favored : 81.74 % 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: -1.84 (0.26), residues: 1074 helix: -0.48 (0.25), residues: 463 sheet: -3.82 (0.92), residues: 20 loop : -1.76 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.013 0.001 PHE A 332 TYR 0.024 0.001 TYR B 638 ARG 0.002 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.17 seconds wall clock time: 30 minutes 56.24 seconds (1856.24 seconds total)