Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:57:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/12_2022/8bc0_15958.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5611 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 30, 'TRANS': 649} Chain breaks: 9 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5244 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 27, 'TRANS': 608} Chain breaks: 9 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.37, per 1000 atoms: 0.59 Number of scatterers: 10861 At special positions: 0 Unit cell: (75.516, 113.274, 127.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 71 16.00 O 1875 8.00 N 1749 7.00 C 7160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.600A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.945A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.845A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.405A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.724A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.578A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.692A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.566A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.663A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.991A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.528A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.695A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.287A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.864A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.530A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.577A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.610A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.719A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 361 through 375 removed outlier: 4.069A pdb=" N LYS B 369 " --> pdb=" O CYS B 365 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.728A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 475 Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.922A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.923A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.944A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.819A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.952A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.654A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.559A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.646A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.393A pdb=" N MET B 348 " --> pdb=" O TRP B 359 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 673 hydrogen bonds defined for protein. 1992 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: 3.42 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3284 1.34 - 1.46: 2919 1.46 - 1.58: 4841 1.58 - 1.70: 1 1.70 - 1.82: 108 Bond restraints: 11153 Sorted by residual: bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.528 1.589 -0.060 2.61e-02 1.47e+03 5.33e+00 bond pdb=" C ASP A 583 " pdb=" O ASP A 583 " ideal model delta sigma weight residual 1.235 1.246 -0.011 4.70e-03 4.53e+04 5.25e+00 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" CG LEU B 836 " pdb=" CD1 LEU B 836 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.35e-02 5.49e+03 1.25e+00 ... (remaining 11148 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.43: 323 106.43 - 113.35: 5918 113.35 - 120.27: 4191 120.27 - 127.20: 4549 127.20 - 134.12: 135 Bond angle restraints: 15116 Sorted by residual: angle pdb=" N ALA B 834 " pdb=" CA ALA B 834 " pdb=" C ALA B 834 " ideal model delta sigma weight residual 111.07 118.18 -7.11 1.07e+00 8.73e-01 4.41e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta sigma weight residual 110.30 119.41 -9.11 1.54e+00 4.22e-01 3.50e+01 angle pdb=" N LYS B 835 " pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 111.82 117.11 -5.29 1.16e+00 7.43e-01 2.08e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" C LEU B 836 " ideal model delta sigma weight residual 112.23 106.55 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C LYS B 835 " pdb=" CA LYS B 835 " pdb=" CB LYS B 835 " ideal model delta sigma weight residual 110.67 103.41 7.26 1.92e+00 2.71e-01 1.43e+01 ... (remaining 15111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 5948 16.50 - 33.01: 439 33.01 - 49.51: 129 49.51 - 66.02: 30 66.02 - 82.52: 2 Dihedral angle restraints: 6548 sinusoidal: 2662 harmonic: 3886 Sorted by residual: dihedral pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta harmonic sigma weight residual 122.80 131.89 -9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA ARG A 712 " pdb=" C ARG A 712 " pdb=" N ARG A 713 " pdb=" CA ARG A 713 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 121.55 -28.55 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 6545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1404 0.058 - 0.116: 243 0.116 - 0.173: 5 0.173 - 0.231: 1 0.231 - 0.289: 2 Chirality restraints: 1655 Sorted by residual: chirality pdb=" CA ALA B 834 " pdb=" N ALA B 834 " pdb=" C ALA B 834 " pdb=" CB ALA B 834 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU B 836 " pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CB LEU B 836 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA PRO A 752 " pdb=" N PRO A 752 " pdb=" C PRO A 752 " pdb=" CB PRO A 752 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1652 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 685 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 686 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 757 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C TYR B 757 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR B 757 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP B 758 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 246 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 247 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.032 5.00e-02 4.00e+02 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 181 2.62 - 3.19: 10641 3.19 - 3.76: 18021 3.76 - 4.33: 24202 4.33 - 4.90: 38741 Nonbonded interactions: 91786 Sorted by model distance: nonbonded pdb=" OE2 GLU A 667 " pdb="CA CA A1002 " model vdw 2.052 2.510 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.127 2.440 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1001 " model vdw 2.195 2.510 nonbonded pdb=" O TYR A 291 " pdb=" NH2 ARG A 713 " model vdw 2.197 2.520 nonbonded pdb=" OD1 ASP A 703 " pdb="CA CA A1002 " model vdw 2.198 2.510 ... (remaining 91781 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 50 through 120 or resid 122 through 414 or resid 451 throu \ gh 475 or resid 509 through 638 or resid 645 through 788 or resid 805 through 87 \ 0 or resid 1001 through 1003)) selection = (chain 'B' and (resid 50 through 587 or resid 591 through 870 or resid 1001 thro \ ugh 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 71 5.16 5 C 7160 2.51 5 N 1749 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 4.830 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 31.710 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 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 0.060 11153 Z= 0.262 Angle : 0.586 9.111 15116 Z= 0.330 Chirality : 0.041 0.289 1655 Planarity : 0.005 0.061 1862 Dihedral : 13.165 82.524 4027 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 7.06 % 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: 0.18 (0.23), residues: 1276 helix: 1.08 (0.18), residues: 810 sheet: -1.10 (0.69), residues: 50 loop : -1.62 (0.31), residues: 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 298 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 37 residues processed: 363 average time/residue: 0.2277 time to fit residues: 116.6789 Evaluate side-chains 254 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1157 time to fit residues: 8.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 205 ASN A 275 HIS ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 99 GLN B 111 GLN B 328 GLN B 351 GLN B 401 GLN B 710 GLN B 730 GLN B 779 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11153 Z= 0.217 Angle : 0.617 10.732 15116 Z= 0.325 Chirality : 0.042 0.188 1655 Planarity : 0.005 0.070 1862 Dihedral : 4.514 17.024 1445 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 2.55 % 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: 0.37 (0.23), residues: 1276 helix: 1.22 (0.18), residues: 816 sheet: -1.02 (0.68), residues: 50 loop : -1.57 (0.30), residues: 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 256 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 276 average time/residue: 0.2160 time to fit residues: 85.9197 Evaluate side-chains 219 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1069 time to fit residues: 4.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 11153 Z= 0.289 Angle : 0.651 11.412 15116 Z= 0.346 Chirality : 0.044 0.222 1655 Planarity : 0.006 0.063 1862 Dihedral : 4.711 18.960 1445 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.98 % 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: 0.08 (0.23), residues: 1276 helix: 1.00 (0.17), residues: 817 sheet: -1.15 (0.66), residues: 51 loop : -1.70 (0.30), residues: 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 249 average time/residue: 0.2023 time to fit residues: 73.7997 Evaluate side-chains 220 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0994 time to fit residues: 4.6174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 126 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11153 Z= 0.213 Angle : 0.614 11.004 15116 Z= 0.324 Chirality : 0.041 0.227 1655 Planarity : 0.005 0.059 1862 Dihedral : 4.589 19.434 1445 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1276 helix: 1.05 (0.17), residues: 816 sheet: -0.83 (0.70), residues: 51 loop : -1.68 (0.30), residues: 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 236 average time/residue: 0.2074 time to fit residues: 71.8018 Evaluate side-chains 218 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1094 time to fit residues: 4.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.0980 chunk 71 optimal weight: 0.0970 chunk 1 optimal weight: 0.0030 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11153 Z= 0.172 Angle : 0.589 10.385 15116 Z= 0.311 Chirality : 0.041 0.197 1655 Planarity : 0.005 0.060 1862 Dihedral : 4.420 18.937 1445 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.28 % 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: 0.32 (0.23), residues: 1276 helix: 1.15 (0.17), residues: 825 sheet: 0.03 (0.82), residues: 41 loop : -1.69 (0.30), residues: 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 238 average time/residue: 0.1979 time to fit residues: 69.6164 Evaluate side-chains 206 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1068 time to fit residues: 3.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 562 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 11153 Z= 0.328 Angle : 0.702 13.579 15116 Z= 0.372 Chirality : 0.045 0.345 1655 Planarity : 0.006 0.065 1862 Dihedral : 4.801 22.192 1445 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.79 % 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: -0.07 (0.23), residues: 1276 helix: 0.83 (0.17), residues: 823 sheet: -0.65 (0.76), residues: 46 loop : -1.74 (0.30), residues: 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 223 average time/residue: 0.2066 time to fit residues: 66.8269 Evaluate side-chains 197 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0950 time to fit residues: 3.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 562 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 11153 Z= 0.237 Angle : 0.662 12.262 15116 Z= 0.351 Chirality : 0.043 0.217 1655 Planarity : 0.006 0.064 1862 Dihedral : 4.697 21.341 1445 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.77 % 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: -0.07 (0.23), residues: 1276 helix: 0.83 (0.17), residues: 827 sheet: -0.28 (0.78), residues: 41 loop : -1.82 (0.30), residues: 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 222 average time/residue: 0.2094 time to fit residues: 67.9752 Evaluate side-chains 195 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0986 time to fit residues: 2.5699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11153 Z= 0.217 Angle : 0.660 13.009 15116 Z= 0.346 Chirality : 0.042 0.218 1655 Planarity : 0.005 0.064 1862 Dihedral : 4.631 19.873 1445 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1276 helix: 0.88 (0.17), residues: 825 sheet: -0.19 (0.78), residues: 41 loop : -1.81 (0.30), residues: 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 205 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.2161 time to fit residues: 66.0381 Evaluate side-chains 205 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0971 time to fit residues: 2.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11153 Z= 0.216 Angle : 0.670 11.415 15116 Z= 0.353 Chirality : 0.043 0.233 1655 Planarity : 0.006 0.069 1862 Dihedral : 4.619 19.689 1445 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.34 % 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: 0.02 (0.23), residues: 1276 helix: 0.90 (0.18), residues: 822 sheet: -0.92 (0.67), residues: 51 loop : -1.67 (0.31), residues: 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 204 average time/residue: 0.2143 time to fit residues: 64.5658 Evaluate side-chains 199 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1047 time to fit residues: 2.9162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 99 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11153 Z= 0.229 Angle : 0.687 14.620 15116 Z= 0.358 Chirality : 0.043 0.227 1655 Planarity : 0.005 0.068 1862 Dihedral : 4.677 19.959 1445 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.17 % 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: -0.04 (0.23), residues: 1276 helix: 0.89 (0.18), residues: 824 sheet: -0.92 (0.66), residues: 51 loop : -1.79 (0.30), residues: 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 199 average time/residue: 0.2134 time to fit residues: 62.0832 Evaluate side-chains 194 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0994 time to fit residues: 2.1707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.226595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.204660 restraints weight = 21656.015| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 2.97 r_work: 0.4518 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11153 Z= 0.234 Angle : 0.695 13.700 15116 Z= 0.363 Chirality : 0.043 0.223 1655 Planarity : 0.006 0.071 1862 Dihedral : 4.704 19.680 1445 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.26 % 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: -0.06 (0.23), residues: 1276 helix: 0.88 (0.18), residues: 822 sheet: -0.98 (0.65), residues: 51 loop : -1.81 (0.30), residues: 403 =============================================================================== Job complete usr+sys time: 2461.57 seconds wall clock time: 45 minutes 37.71 seconds (2737.71 seconds total)