Starting phenix.real_space_refine on Thu Feb 15 03:52:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xul_33473/02_2024/7xul_33473.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 C 7346 2.51 5 N 1754 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ASP 617": "OD1" <-> "OD2" Residue "A ASP 624": "OD1" <-> "OD2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ASP 617": "OD1" <-> "OD2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B ASP 633": "OD1" <-> "OD2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B ASP 701": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5380 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 3 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5380 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 3 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'I2U': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'I2U': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.42, per 1000 atoms: 0.58 Number of scatterers: 11082 At special positions: 0 Unit cell: (91.545, 128.163, 103.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 42 16.00 O 1938 8.00 N 1754 7.00 C 7346 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: 7.18 Conformation dependent library (CDL) restraints added in 2.4 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 61.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.085A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.930A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 95 removed outlier: 6.275A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.633A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.543A pdb=" N SER A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 196 removed outlier: 4.016A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.633A pdb=" N TYR A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.848A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.904A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.862A pdb=" N THR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 341 through 364 removed outlier: 3.821A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.639A pdb=" N GLU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.670A pdb=" N LEU A 432 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.927A pdb=" N ARG A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.697A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 585 Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.786A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.698A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.590A pdb=" N HIS A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 46 through 58 removed outlier: 4.085A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.931A pdb=" N TRP B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 95 removed outlier: 6.276A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.634A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.543A pdb=" N SER B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 196 removed outlier: 4.015A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.632A pdb=" N TYR B 204 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.847A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.904A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 281 removed outlier: 3.863A pdb=" N THR B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 341 through 364 removed outlier: 3.821A pdb=" N GLY B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.639A pdb=" N GLU B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.670A pdb=" N LEU B 432 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.928A pdb=" N ARG B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 484 through 503 removed outlier: 3.697A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 585 Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.785A pdb=" N VAL B 615 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.698A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 713 through 725 removed outlier: 3.590A pdb=" N HIS B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.549A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.758A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.550A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1737 1.32 - 1.44: 2842 1.44 - 1.56: 6687 1.56 - 1.69: 8 1.69 - 1.81: 62 Bond restraints: 11336 Sorted by residual: bond pdb=" C13 I2U B 803 " pdb=" C9 I2U B 803 " ideal model delta sigma weight residual 1.386 1.613 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C13 I2U A 801 " pdb=" C9 I2U A 801 " ideal model delta sigma weight residual 1.386 1.612 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C12 I2U A 801 " pdb=" C8 I2U A 801 " ideal model delta sigma weight residual 1.393 1.597 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 I2U B 803 " pdb=" C8 I2U B 803 " ideal model delta sigma weight residual 1.393 1.597 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C21 I2U B 803 " pdb=" S2 I2U B 803 " ideal model delta sigma weight residual 1.705 1.521 0.184 2.00e-02 2.50e+03 8.45e+01 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.11: 233 105.11 - 112.35: 5747 112.35 - 119.59: 4026 119.59 - 126.83: 5305 126.83 - 134.08: 121 Bond angle restraints: 15432 Sorted by residual: angle pdb=" C18 I2U B 803 " pdb=" S2 I2U B 803 " pdb=" C21 I2U B 803 " ideal model delta sigma weight residual 91.76 107.91 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C18 I2U A 801 " pdb=" S2 I2U A 801 " pdb=" C21 I2U A 801 " ideal model delta sigma weight residual 91.76 107.88 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" N ILE A 549 " pdb=" CA ILE A 549 " pdb=" C ILE A 549 " ideal model delta sigma weight residual 111.81 108.55 3.26 8.60e-01 1.35e+00 1.44e+01 angle pdb=" N ILE B 549 " pdb=" CA ILE B 549 " pdb=" C ILE B 549 " ideal model delta sigma weight residual 111.81 108.57 3.24 8.60e-01 1.35e+00 1.42e+01 angle pdb=" C LEU B 637 " pdb=" N ASN B 638 " pdb=" CA ASN B 638 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 ... (remaining 15427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 6247 15.44 - 30.88: 683 30.88 - 46.32: 160 46.32 - 61.76: 30 61.76 - 77.20: 12 Dihedral angle restraints: 7132 sinusoidal: 3136 harmonic: 3996 Sorted by residual: dihedral pdb=" CA PRO B 240 " pdb=" C PRO B 240 " pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta harmonic sigma weight residual 180.00 -120.11 -59.89 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA PRO A 240 " pdb=" C PRO A 240 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " ideal model delta harmonic sigma weight residual -180.00 -120.16 -59.84 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA ASP B 239 " pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 7129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1328 0.053 - 0.105: 433 0.105 - 0.158: 71 0.158 - 0.211: 6 0.211 - 0.263: 8 Chirality restraints: 1846 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU B 671 " pdb=" CB LEU B 671 " pdb=" CD1 LEU B 671 " pdb=" CD2 LEU B 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1843 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 240 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C PRO B 240 " 0.058 2.00e-02 2.50e+03 pdb=" O PRO B 240 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL B 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 240 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO A 240 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO A 240 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL A 241 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 239 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO B 240 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " -0.044 5.00e-02 4.00e+02 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3653 2.84 - 3.36: 9905 3.36 - 3.87: 17478 3.87 - 4.39: 20042 4.39 - 4.90: 35203 Nonbonded interactions: 86281 Sorted by model distance: nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.330 2.440 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.330 2.440 nonbonded pdb=" OG SER A 75 " pdb=" O GLY A 407 " model vdw 2.337 2.440 nonbonded pdb=" OG SER B 75 " pdb=" O GLY B 407 " model vdw 2.337 2.440 nonbonded pdb=" OH TYR B 116 " pdb=" OE1 GLU B 374 " model vdw 2.350 2.440 ... (remaining 86276 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 8 through 725 or resid 802 or resid 804 through 805)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 7.390 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.500 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.009 0.227 11336 Z= 0.564 Angle : 0.855 16.155 15432 Z= 0.461 Chirality : 0.052 0.263 1846 Planarity : 0.008 0.080 1876 Dihedral : 13.639 77.198 4548 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 0.34 % Allowed : 6.73 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.15 % 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: -3.95 (0.18), residues: 1364 helix: -2.26 (0.14), residues: 810 sheet: 0.07 (0.80), residues: 34 loop : -3.27 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 PHE 0.021 0.002 PHE B 130 TYR 0.024 0.002 TYR B 9 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.390 Fit side-chains REVERT: A 280 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 449 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5329 (mmtt) REVERT: A 545 TYR cc_start: 0.8642 (p90) cc_final: 0.8376 (p90) REVERT: A 640 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 280 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 474 MET cc_start: 0.8928 (mmm) cc_final: 0.8722 (mmt) REVERT: B 545 TYR cc_start: 0.8898 (p90) cc_final: 0.8655 (p90) REVERT: B 638 ASN cc_start: 0.6890 (p0) cc_final: 0.6525 (p0) REVERT: B 640 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7810 (tm-30) outliers start: 4 outliers final: 0 residues processed: 117 average time/residue: 0.2582 time to fit residues: 42.7969 Evaluate side-chains 73 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 338 ASN A 504 GLN B 90 GLN B 225 GLN B 326 GLN B 338 ASN B 504 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11336 Z= 0.190 Angle : 0.530 6.617 15432 Z= 0.275 Chirality : 0.041 0.136 1846 Planarity : 0.005 0.073 1876 Dihedral : 7.615 54.518 2048 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.40 % Favored : 95.38 % Rotamer: Outliers : 1.09 % Allowed : 11.45 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.57 (0.22), residues: 1364 helix: -0.08 (0.18), residues: 790 sheet: 0.98 (0.81), residues: 34 loop : -2.68 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 647 PHE 0.016 0.001 PHE B 130 TYR 0.011 0.001 TYR B 367 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.269 Fit side-chains REVERT: A 449 LYS cc_start: 0.5746 (mmtt) cc_final: 0.5056 (mmtt) REVERT: B 280 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 326 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: B 545 TYR cc_start: 0.8930 (p90) cc_final: 0.8727 (p90) REVERT: B 640 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7769 (tm-30) outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 0.1895 time to fit residues: 27.3285 Evaluate side-chains 83 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 326 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 0.0050 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 0.0370 chunk 111 optimal weight: 0.0470 chunk 124 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11336 Z= 0.113 Angle : 0.469 6.794 15432 Z= 0.241 Chirality : 0.039 0.144 1846 Planarity : 0.004 0.074 1876 Dihedral : 6.980 53.932 2048 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.74 (0.24), residues: 1364 helix: 0.51 (0.19), residues: 814 sheet: 1.59 (0.83), residues: 34 loop : -2.32 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.001 0.000 HIS B 220 PHE 0.015 0.001 PHE B 130 TYR 0.010 0.001 TYR A 545 ARG 0.005 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.445 Fit side-chains REVERT: A 449 LYS cc_start: 0.5607 (mmtt) cc_final: 0.4987 (mmtt) REVERT: A 640 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 545 TYR cc_start: 0.8861 (p90) cc_final: 0.8621 (p90) REVERT: B 640 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7586 (tm-30) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.1959 time to fit residues: 30.1420 Evaluate side-chains 94 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11336 Z= 0.228 Angle : 0.524 7.705 15432 Z= 0.263 Chirality : 0.041 0.158 1846 Planarity : 0.004 0.074 1876 Dihedral : 6.799 50.289 2048 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 2.10 % Allowed : 11.53 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.15 (0.24), residues: 1364 helix: 1.03 (0.20), residues: 802 sheet: 1.97 (0.86), residues: 34 loop : -2.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 63 HIS 0.004 0.001 HIS A 714 PHE 0.019 0.001 PHE A 130 TYR 0.015 0.001 TYR A 9 ARG 0.002 0.000 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.256 Fit side-chains REVERT: A 326 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: A 449 LYS cc_start: 0.5733 (mmtt) cc_final: 0.5258 (mmtt) REVERT: A 640 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 193 PHE cc_start: 0.8896 (m-10) cc_final: 0.8467 (m-80) REVERT: B 640 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7578 (tm-30) outliers start: 25 outliers final: 14 residues processed: 91 average time/residue: 0.1649 time to fit residues: 24.5810 Evaluate side-chains 92 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11336 Z= 0.223 Angle : 0.511 7.522 15432 Z= 0.258 Chirality : 0.041 0.155 1846 Planarity : 0.004 0.072 1876 Dihedral : 6.738 48.831 2048 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.19 % Allowed : 12.63 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.04 (0.24), residues: 1364 helix: 1.22 (0.20), residues: 798 sheet: 2.13 (0.85), residues: 34 loop : -2.07 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS A 714 PHE 0.018 0.001 PHE B 130 TYR 0.012 0.001 TYR A 9 ARG 0.001 0.000 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 1.248 Fit side-chains REVERT: A 449 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5336 (mmtt) REVERT: A 640 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 612 GLN cc_start: 0.8769 (tt0) cc_final: 0.8469 (tt0) REVERT: B 640 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 26 outliers final: 23 residues processed: 91 average time/residue: 0.1817 time to fit residues: 26.7383 Evaluate side-chains 98 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11336 Z= 0.241 Angle : 0.517 7.566 15432 Z= 0.261 Chirality : 0.041 0.151 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.713 46.806 2048 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.61 % Allowed : 12.63 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.12 (0.24), residues: 1364 helix: 1.18 (0.20), residues: 826 sheet: 2.19 (0.85), residues: 34 loop : -2.02 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS A 714 PHE 0.017 0.001 PHE A 130 TYR 0.014 0.001 TYR A 9 ARG 0.002 0.000 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.277 Fit side-chains REVERT: A 449 LYS cc_start: 0.6020 (mmtt) cc_final: 0.5245 (mmtt) REVERT: A 453 MET cc_start: 0.8664 (mmm) cc_final: 0.8424 (mmm) REVERT: A 640 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 640 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7549 (tm-30) outliers start: 31 outliers final: 24 residues processed: 92 average time/residue: 0.1836 time to fit residues: 27.3506 Evaluate side-chains 99 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 0.0070 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11336 Z= 0.158 Angle : 0.483 7.186 15432 Z= 0.245 Chirality : 0.040 0.151 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.597 46.809 2048 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 14.56 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.31 (0.24), residues: 1364 helix: 1.32 (0.20), residues: 824 sheet: 2.33 (0.87), residues: 34 loop : -1.90 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 647 PHE 0.015 0.001 PHE A 130 TYR 0.009 0.001 TYR B 367 ARG 0.001 0.000 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.362 Fit side-chains REVERT: A 449 LYS cc_start: 0.6012 (mmtt) cc_final: 0.5261 (mmtt) REVERT: A 638 ASN cc_start: 0.7110 (p0) cc_final: 0.6821 (p0) REVERT: A 640 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 612 GLN cc_start: 0.8750 (tt0) cc_final: 0.8460 (tt0) REVERT: B 640 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 22 outliers final: 19 residues processed: 96 average time/residue: 0.1863 time to fit residues: 28.6391 Evaluate side-chains 100 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11336 Z= 0.197 Angle : 0.491 7.312 15432 Z= 0.248 Chirality : 0.040 0.148 1846 Planarity : 0.004 0.070 1876 Dihedral : 6.574 46.373 2048 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.02 % Allowed : 14.73 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.39 (0.24), residues: 1364 helix: 1.38 (0.20), residues: 824 sheet: 2.42 (0.86), residues: 34 loop : -1.87 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS B 220 PHE 0.018 0.001 PHE B 130 TYR 0.010 0.001 TYR B 9 ARG 0.003 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.409 Fit side-chains REVERT: A 453 MET cc_start: 0.8629 (mmm) cc_final: 0.8401 (mmm) REVERT: A 640 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 612 GLN cc_start: 0.8759 (tt0) cc_final: 0.8466 (tt0) REVERT: B 640 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7488 (tm-30) outliers start: 24 outliers final: 17 residues processed: 91 average time/residue: 0.1694 time to fit residues: 25.4260 Evaluate side-chains 94 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 0.0030 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 117 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11336 Z= 0.139 Angle : 0.480 7.918 15432 Z= 0.248 Chirality : 0.040 0.156 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.455 46.168 2048 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 1.52 % Allowed : 14.90 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.56 (0.25), residues: 1364 helix: 1.51 (0.20), residues: 822 sheet: 2.51 (0.87), residues: 34 loop : -1.77 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.000 HIS A 647 PHE 0.016 0.001 PHE B 130 TYR 0.009 0.001 TYR A 367 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.250 Fit side-chains REVERT: A 453 MET cc_start: 0.8636 (mmm) cc_final: 0.8417 (mmm) REVERT: A 640 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 640 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.1744 time to fit residues: 25.8581 Evaluate side-chains 92 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 11 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11336 Z= 0.154 Angle : 0.482 7.707 15432 Z= 0.247 Chirality : 0.040 0.151 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.421 46.470 2048 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 1.43 % Allowed : 15.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.66 (0.25), residues: 1364 helix: 1.59 (0.20), residues: 820 sheet: 2.56 (0.87), residues: 34 loop : -1.71 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 PHE 0.017 0.001 PHE B 130 TYR 0.010 0.001 TYR A 367 ARG 0.002 0.000 ARG A 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.367 Fit side-chains REVERT: A 453 MET cc_start: 0.8652 (mmm) cc_final: 0.8427 (mmm) REVERT: A 640 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 640 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7487 (tm-30) outliers start: 17 outliers final: 16 residues processed: 84 average time/residue: 0.1798 time to fit residues: 24.9169 Evaluate side-chains 90 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.073611 restraints weight = 18741.868| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.44 r_work: 0.2723 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11336 Z= 0.171 Angle : 0.486 7.379 15432 Z= 0.249 Chirality : 0.040 0.151 1846 Planarity : 0.004 0.066 1876 Dihedral : 6.417 46.878 2048 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 1.52 % Allowed : 15.32 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.74 (0.25), residues: 1364 helix: 1.65 (0.20), residues: 822 sheet: 2.62 (0.87), residues: 34 loop : -1.70 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS B 220 PHE 0.017 0.001 PHE B 130 TYR 0.010 0.001 TYR A 367 ARG 0.002 0.000 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.76 seconds wall clock time: 41 minutes 42.30 seconds (2502.30 seconds total)