Starting phenix.real_space_refine on Wed Nov 15 19:06:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw2_26148/11_2023/7tw2_26148.pdb" } resolution = 4.8 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8429 2.51 5 N 2122 2.21 5 O 2239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12838 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6435 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 3 Chain: "A" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6375 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 47, 'TRANS': 757} Chain breaks: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.01, per 1000 atoms: 0.55 Number of scatterers: 12838 At special positions: 0 Unit cell: (120.006, 96.642, 147.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2239 8.00 N 2122 7.00 C 8429 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 Links applied NAG-ASN " NAG A1000 " - " ASN A 642 " " NAG B1000 " - " ASN B 642 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.4 seconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 61.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.084A pdb=" N LYS B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.975A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.265A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 335 through 349 removed outlier: 4.116A pdb=" N SER B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 4.062A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.684A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.622A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.667A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.615A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.976A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.529A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.734A pdb=" N ALA B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.597A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 786 through 799 removed outlier: 3.987A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.675A pdb=" N ASP B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.580A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.698A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.617A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.826A pdb=" N GLU A 168 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.507A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.578A pdb=" N GLU A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 4.025A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.553A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 4.016A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.731A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.574A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.706A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.662A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.862A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.522A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.530A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.635A pdb=" N ALA A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.832A pdb=" N LYS A 695 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 786 through 799 removed outlier: 3.980A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.579A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.784A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 removed outlier: 3.635A pdb=" N LEU A 835 " --> pdb=" O TRP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.947A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67 removed outlier: 6.585A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 87 current: chain 'B' and resid 226 through 234 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 226 through 234 current: chain 'B' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.620A pdb=" N LEU B 319 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 319 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 67 removed outlier: 7.025A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 86 through 87 current: chain 'A' and resid 262 through 269 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.747A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1950 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: 3.60 Time building geometry restraints manager: 5.37 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: 4038 1.34 - 1.46: 2842 1.46 - 1.58: 6176 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 13142 Sorted by residual: bond pdb=" N LEU B 706 " pdb=" CA LEU B 706 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.91e+00 bond pdb=" N TRP B 662 " pdb=" CA TRP B 662 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C VAL A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 ... (remaining 13137 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.66: 283 104.66 - 112.07: 6664 112.07 - 119.47: 4409 119.47 - 126.88: 6314 126.88 - 134.28: 189 Bond angle restraints: 17859 Sorted by residual: angle pdb=" N TRP B 662 " pdb=" CA TRP B 662 " pdb=" C TRP B 662 " ideal model delta sigma weight residual 111.36 107.14 4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N LYS A 695 " pdb=" CA LYS A 695 " pdb=" C LYS A 695 " ideal model delta sigma weight residual 111.30 116.42 -5.12 1.36e+00 5.41e-01 1.42e+01 angle pdb=" CB MET B 586 " pdb=" CG MET B 586 " pdb=" SD MET B 586 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA GLU B 254 " pdb=" CB GLU B 254 " pdb=" CG GLU B 254 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET B 712 " pdb=" CG MET B 712 " pdb=" SD MET B 712 " ideal model delta sigma weight residual 112.70 122.19 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 17854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7146 17.95 - 35.91: 573 35.91 - 53.86: 88 53.86 - 71.81: 12 71.81 - 89.76: 18 Dihedral angle restraints: 7837 sinusoidal: 3160 harmonic: 4677 Sorted by residual: dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 555 " pdb=" C TYR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR B 555 " pdb=" C TYR B 555 " pdb=" N ASN B 556 " pdb=" CA ASN B 556 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1722 0.057 - 0.113: 332 0.113 - 0.170: 38 0.170 - 0.226: 2 0.226 - 0.283: 1 Chirality restraints: 2095 Sorted by residual: chirality pdb=" CA MET B 300 " pdb=" N MET B 300 " pdb=" C MET B 300 " pdb=" CB MET B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA LYS A 219 " pdb=" N LYS A 219 " pdb=" C LYS A 219 " pdb=" CB LYS A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE B 296 " pdb=" CA ILE B 296 " pdb=" CG1 ILE B 296 " pdb=" CG2 ILE B 296 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 2092 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 447 " -0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C GLN B 447 " 0.080 2.00e-02 2.50e+03 pdb=" O GLN B 447 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 448 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 831 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C TRP B 831 " 0.077 2.00e-02 2.50e+03 pdb=" O TRP B 831 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 832 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 197 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C THR A 197 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 197 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 198 " -0.019 2.00e-02 2.50e+03 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 611 2.72 - 3.27: 12954 3.27 - 3.81: 20545 3.81 - 4.36: 24058 4.36 - 4.90: 41847 Nonbonded interactions: 100015 Sorted by model distance: nonbonded pdb=" OE2 GLU B 63 " pdb=" OG1 THR B 279 " model vdw 2.177 2.440 nonbonded pdb=" NH1 ARG A 646 " pdb=" O GLY A 647 " model vdw 2.207 2.520 nonbonded pdb=" ND2 ASN B 569 " pdb=" O PRO A 568 " model vdw 2.216 2.520 nonbonded pdb=" OE2 GLU B 291 " pdb=" NE ARG B 346 " model vdw 2.257 2.520 nonbonded pdb=" NH1 ARG B 646 " pdb=" O GLY B 647 " model vdw 2.260 2.520 ... (remaining 100010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 55 through 348 or resid 369 through 894 or resid 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 7.610 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.280 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.003 0.030 13142 Z= 0.188 Angle : 0.749 10.273 17859 Z= 0.377 Chirality : 0.043 0.283 2095 Planarity : 0.005 0.058 2240 Dihedral : 13.684 89.764 4807 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1603 helix: 0.08 (0.17), residues: 903 sheet: -0.26 (0.54), residues: 85 loop : -2.33 (0.20), residues: 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.2004 time to fit residues: 26.0501 Evaluate side-chains 56 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 41 optimal weight: 20.0000 chunk 82 optimal weight: 0.0470 chunk 65 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 0.0980 chunk 146 optimal weight: 5.9990 overall best weight: 2.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13142 Z= 0.183 Angle : 0.573 6.769 17859 Z= 0.276 Chirality : 0.039 0.143 2095 Planarity : 0.004 0.050 2240 Dihedral : 3.756 20.869 1735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1603 helix: 1.42 (0.17), residues: 925 sheet: 0.38 (0.57), residues: 84 loop : -1.59 (0.21), residues: 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2131 time to fit residues: 23.9823 Evaluate side-chains 52 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 50.0000 chunk 45 optimal weight: 8.9990 chunk 121 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 158 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13142 Z= 0.249 Angle : 0.638 7.317 17859 Z= 0.312 Chirality : 0.040 0.174 2095 Planarity : 0.005 0.041 2240 Dihedral : 4.020 22.862 1735 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.23 % 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: 0.75 (0.21), residues: 1603 helix: 1.50 (0.17), residues: 936 sheet: 0.27 (0.56), residues: 81 loop : -1.12 (0.23), residues: 586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2084 time to fit residues: 22.8015 Evaluate side-chains 50 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13142 Z= 0.201 Angle : 0.583 7.219 17859 Z= 0.283 Chirality : 0.039 0.178 2095 Planarity : 0.004 0.038 2240 Dihedral : 3.924 22.221 1735 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1603 helix: 1.73 (0.17), residues: 942 sheet: 0.21 (0.55), residues: 82 loop : -0.91 (0.24), residues: 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2063 time to fit residues: 22.3372 Evaluate side-chains 52 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13142 Z= 0.274 Angle : 0.666 7.462 17859 Z= 0.327 Chirality : 0.041 0.213 2095 Planarity : 0.004 0.037 2240 Dihedral : 4.253 21.707 1735 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1603 helix: 1.55 (0.17), residues: 942 sheet: 0.14 (0.56), residues: 81 loop : -0.82 (0.24), residues: 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2269 time to fit residues: 23.0823 Evaluate side-chains 51 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 150 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13142 Z= 0.248 Angle : 0.633 7.110 17859 Z= 0.311 Chirality : 0.040 0.166 2095 Planarity : 0.004 0.039 2240 Dihedral : 4.299 21.919 1735 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.95 (0.21), residues: 1603 helix: 1.51 (0.17), residues: 939 sheet: 0.02 (0.56), residues: 84 loop : -0.69 (0.24), residues: 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.405 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2109 time to fit residues: 21.3673 Evaluate side-chains 50 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 GLN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13142 Z= 0.252 Angle : 0.653 7.023 17859 Z= 0.322 Chirality : 0.041 0.160 2095 Planarity : 0.005 0.057 2240 Dihedral : 4.397 22.283 1735 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 0.93 (0.21), residues: 1603 helix: 1.45 (0.17), residues: 937 sheet: 0.09 (0.56), residues: 84 loop : -0.62 (0.25), residues: 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.548 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2327 time to fit residues: 23.6439 Evaluate side-chains 51 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 50.0000 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13142 Z= 0.162 Angle : 0.595 13.712 17859 Z= 0.281 Chirality : 0.040 0.202 2095 Planarity : 0.004 0.047 2240 Dihedral : 4.155 21.712 1735 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1603 helix: 1.84 (0.17), residues: 936 sheet: 0.27 (0.56), residues: 84 loop : -0.48 (0.25), residues: 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.382 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1985 time to fit residues: 21.2128 Evaluate side-chains 51 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13142 Z= 0.316 Angle : 0.730 10.639 17859 Z= 0.362 Chirality : 0.042 0.192 2095 Planarity : 0.005 0.050 2240 Dihedral : 4.614 22.038 1735 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 0.76 (0.21), residues: 1603 helix: 1.26 (0.17), residues: 934 sheet: 0.13 (0.57), residues: 84 loop : -0.60 (0.24), residues: 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.631 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2200 time to fit residues: 21.9567 Evaluate side-chains 49 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13142 Z= 0.145 Angle : 0.608 11.346 17859 Z= 0.284 Chirality : 0.040 0.179 2095 Planarity : 0.004 0.043 2240 Dihedral : 4.198 21.729 1735 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1603 helix: 1.88 (0.17), residues: 934 sheet: 0.30 (0.58), residues: 84 loop : -0.51 (0.25), residues: 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.484 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2035 time to fit residues: 22.7243 Evaluate side-chains 50 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 50.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 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 = 0.3718 r_free = 0.3718 target = 0.067327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047022 restraints weight = 130404.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047638 restraints weight = 78285.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.048156 restraints weight = 50921.573| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13142 Z= 0.197 Angle : 0.624 10.617 17859 Z= 0.299 Chirality : 0.040 0.182 2095 Planarity : 0.004 0.052 2240 Dihedral : 4.206 22.043 1735 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1603 helix: 1.80 (0.17), residues: 936 sheet: 0.39 (0.57), residues: 84 loop : -0.52 (0.24), residues: 583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.65 seconds wall clock time: 40 minutes 21.64 seconds (2421.64 seconds total)