Starting phenix.real_space_refine on Sat Dec 9 01:08:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcx_27330/12_2023/8dcx_27330.pdb" } resolution = 2.8 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= 1.000 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 70 5.16 5 C 6141 2.51 5 N 1655 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7621 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 886} Chain breaks: 10 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 2006 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 231} Chain breaks: 1 Time building chain proxies: 5.42, per 1000 atoms: 0.56 Number of scatterers: 9627 At special positions: 0 Unit cell: (84.032, 132.288, 108.16, 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 70 16.00 O 1761 8.00 N 1655 7.00 C 6141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 11 sheets defined 49.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.999A pdb=" N ILE A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.672A pdb=" N MET A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.646A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.662A pdb=" N ALA A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 4.117A pdb=" N LYS A 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.755A pdb=" N VAL A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.045A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.909A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.095A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.930A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 560 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.795A pdb=" N LEU A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.557A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.777A pdb=" N LEU A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 638 removed outlier: 5.327A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.579A pdb=" N ARG A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 718 removed outlier: 4.111A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 4.173A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 removed outlier: 4.216A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 889 removed outlier: 4.086A pdb=" N ILE A 889 " --> pdb=" O LYS A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 889' Processing helix chain 'A' and resid 890 through 911 Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.746A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 removed outlier: 3.662A pdb=" N GLN A 993 " --> pdb=" O LEU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.135A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 4.323A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.752A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 454 through 516 removed outlier: 3.590A pdb=" N GLN B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 582 Proline residue: B 568 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 211 removed outlier: 8.647A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.278A pdb=" N LEU A 339 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU A 385 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 337 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 387 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG A 335 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 389 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 333 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.579A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.557A pdb=" N THR A 358 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 751 through 753 removed outlier: 4.236A pdb=" N PHE A 751 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 449 hydrogen bonds defined for protein. 1260 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: 3.05 Time building geometry restraints manager: 3.90 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: 3137 1.34 - 1.46: 1907 1.46 - 1.58: 4673 1.58 - 1.69: 1 1.69 - 1.81: 110 Bond restraints: 9828 Sorted by residual: bond pdb=" CB PRO B 427 " pdb=" CG PRO B 427 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.77e+00 bond pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.11e+00 bond pdb=" CG PRO B 395 " pdb=" CD PRO B 395 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.64e-01 bond pdb=" CG1 ILE A 894 " pdb=" CD1 ILE A 894 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.61e-01 bond pdb=" CG MET A1004 " pdb=" SD MET A1004 " ideal model delta sigma weight residual 1.803 1.780 0.023 2.50e-02 1.60e+03 8.46e-01 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 165 105.14 - 112.37: 4869 112.37 - 119.60: 3429 119.60 - 126.83: 4652 126.83 - 134.06: 132 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N GLY A 439 " pdb=" CA GLY A 439 " pdb=" C GLY A 439 " ideal model delta sigma weight residual 110.43 114.62 -4.19 1.35e+00 5.49e-01 9.62e+00 angle pdb=" C LEU B 420 " pdb=" N ASP B 421 " pdb=" CA ASP B 421 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.32e+00 angle pdb=" N GLU B 462 " pdb=" CA GLU B 462 " pdb=" CB GLU B 462 " ideal model delta sigma weight residual 110.28 114.90 -4.62 1.55e+00 4.16e-01 8.89e+00 angle pdb=" N GLU A1037 " pdb=" CA GLU A1037 " pdb=" CB GLU A1037 " ideal model delta sigma weight residual 110.28 114.75 -4.47 1.55e+00 4.16e-01 8.32e+00 angle pdb=" CA PRO B 427 " pdb=" N PRO B 427 " pdb=" CD PRO B 427 " ideal model delta sigma weight residual 112.00 108.15 3.85 1.40e+00 5.10e-01 7.55e+00 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5299 18.00 - 36.00: 594 36.00 - 53.99: 85 53.99 - 71.99: 15 71.99 - 89.99: 8 Dihedral angle restraints: 6001 sinusoidal: 2559 harmonic: 3442 Sorted by residual: dihedral pdb=" CA LYS A 440 " pdb=" C LYS A 440 " pdb=" N MET A 441 " pdb=" CA MET A 441 " ideal model delta harmonic sigma weight residual 180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA TYR A 165 " pdb=" C TYR A 165 " pdb=" N VAL A 166 " pdb=" CA VAL A 166 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU A 474 " pdb=" CG GLU A 474 " pdb=" CD GLU A 474 " pdb=" OE1 GLU A 474 " ideal model delta sinusoidal sigma weight residual 0.00 89.28 -89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1208 0.056 - 0.111: 207 0.111 - 0.167: 18 0.167 - 0.223: 2 0.223 - 0.278: 1 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CB ILE A 561 " pdb=" CA ILE A 561 " pdb=" CG1 ILE A 561 " pdb=" CG2 ILE A 561 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 793 " pdb=" CB LEU A 793 " pdb=" CD1 LEU A 793 " pdb=" CD2 LEU A 793 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1433 not shown) Planarity restraints: 1693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 744 " -0.017 2.00e-02 2.50e+03 1.81e-02 5.75e+00 pdb=" CG PHE A 744 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 744 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 744 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 744 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 744 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 744 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 297 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 298 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 710 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU A 710 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 710 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 711 " -0.010 2.00e-02 2.50e+03 ... (remaining 1690 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 660 2.74 - 3.28: 9908 3.28 - 3.82: 15885 3.82 - 4.36: 18308 4.36 - 4.90: 31056 Nonbonded interactions: 75817 Sorted by model distance: nonbonded pdb=" O MET A1005 " pdb=" OG SER A1008 " model vdw 2.195 2.440 nonbonded pdb=" O CYS A 971 " pdb=" OG1 THR A 974 " model vdw 2.255 2.440 nonbonded pdb=" O LEU A 568 " pdb=" OG SER A 571 " model vdw 2.256 2.440 nonbonded pdb=" O HIS A 450 " pdb=" NE2 GLN A1014 " model vdw 2.259 2.520 nonbonded pdb=" O LEU A 367 " pdb=" ND2 ASN A 575 " model vdw 2.259 2.520 ... (remaining 75812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.100 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 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 0.097 9828 Z= 0.211 Angle : 0.584 8.095 13247 Z= 0.309 Chirality : 0.042 0.278 1436 Planarity : 0.004 0.062 1693 Dihedral : 14.710 89.989 3763 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.26), residues: 1140 helix: 0.73 (0.24), residues: 513 sheet: -0.33 (0.50), residues: 123 loop : -0.66 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS A 931 PHE 0.042 0.002 PHE A 744 TYR 0.013 0.001 TYR B 556 ARG 0.006 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 1.0517 time to fit residues: 192.5744 Evaluate side-chains 148 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9828 Z= 0.196 Angle : 0.570 7.185 13247 Z= 0.292 Chirality : 0.041 0.154 1436 Planarity : 0.004 0.065 1693 Dihedral : 4.061 15.873 1275 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.12 % Allowed : 10.44 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.27 (0.26), residues: 1140 helix: 1.06 (0.23), residues: 523 sheet: -0.28 (0.52), residues: 112 loop : -0.58 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 479 HIS 0.004 0.001 HIS A 362 PHE 0.034 0.002 PHE A 744 TYR 0.014 0.001 TYR B 556 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.152 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 168 average time/residue: 1.0607 time to fit residues: 193.6078 Evaluate side-chains 153 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0907 time to fit residues: 1.7544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 380 ASN A 419 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9828 Z= 0.184 Angle : 0.552 6.581 13247 Z= 0.285 Chirality : 0.040 0.155 1436 Planarity : 0.004 0.065 1693 Dihedral : 3.974 16.162 1275 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 1.49 % Allowed : 15.00 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.34 (0.26), residues: 1140 helix: 1.16 (0.24), residues: 526 sheet: -0.27 (0.51), residues: 112 loop : -0.59 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 479 HIS 0.020 0.001 HIS A1047 PHE 0.031 0.002 PHE A 744 TYR 0.034 0.001 TYR A 698 ARG 0.003 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.985 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 166 average time/residue: 1.1525 time to fit residues: 207.0914 Evaluate side-chains 154 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.1879 time to fit residues: 4.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 760 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9828 Z= 0.222 Angle : 0.599 7.954 13247 Z= 0.306 Chirality : 0.041 0.158 1436 Planarity : 0.004 0.066 1693 Dihedral : 4.068 18.609 1275 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 2.05 % Allowed : 17.99 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.26 (0.26), residues: 1140 helix: 1.13 (0.24), residues: 525 sheet: -0.47 (0.47), residues: 123 loop : -0.64 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 574 HIS 0.014 0.001 HIS A1047 PHE 0.029 0.002 PHE A 744 TYR 0.023 0.001 TYR A 165 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 168 average time/residue: 1.1117 time to fit residues: 202.2369 Evaluate side-chains 161 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.9146 time to fit residues: 6.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 28 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 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9828 Z= 0.171 Angle : 0.575 7.250 13247 Z= 0.295 Chirality : 0.040 0.160 1436 Planarity : 0.004 0.064 1693 Dihedral : 3.966 18.102 1275 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.68 % Allowed : 19.01 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.26), residues: 1140 helix: 1.23 (0.24), residues: 524 sheet: -0.32 (0.49), residues: 116 loop : -0.62 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.027 0.001 PHE A 744 TYR 0.021 0.001 TYR A 698 ARG 0.004 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 170 average time/residue: 1.1667 time to fit residues: 215.1141 Evaluate side-chains 161 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.1385 time to fit residues: 4.0142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 112 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 108 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9828 Z= 0.237 Angle : 0.636 9.098 13247 Z= 0.321 Chirality : 0.042 0.157 1436 Planarity : 0.004 0.072 1693 Dihedral : 4.129 19.211 1275 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 1.96 % Allowed : 19.76 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.21 (0.26), residues: 1140 helix: 1.10 (0.24), residues: 523 sheet: -0.62 (0.47), residues: 123 loop : -0.63 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 783 HIS 0.013 0.001 HIS A1047 PHE 0.024 0.002 PHE A 668 TYR 0.018 0.001 TYR A 698 ARG 0.012 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.147 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 173 average time/residue: 1.1002 time to fit residues: 207.1833 Evaluate side-chains 162 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.0311 time to fit residues: 6.0553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.0000 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9828 Z= 0.185 Angle : 0.593 8.958 13247 Z= 0.300 Chirality : 0.041 0.208 1436 Planarity : 0.004 0.063 1693 Dihedral : 4.022 18.443 1275 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 2.24 % Allowed : 20.60 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.23 (0.26), residues: 1140 helix: 1.12 (0.24), residues: 524 sheet: -0.59 (0.46), residues: 126 loop : -0.63 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 783 HIS 0.004 0.001 HIS A 665 PHE 0.031 0.002 PHE A 668 TYR 0.016 0.001 TYR A 698 ARG 0.005 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 170 average time/residue: 1.0736 time to fit residues: 198.4732 Evaluate side-chains 159 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.7095 time to fit residues: 3.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 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 380 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9828 Z= 0.196 Angle : 0.609 8.196 13247 Z= 0.311 Chirality : 0.042 0.203 1436 Planarity : 0.004 0.062 1693 Dihedral : 4.019 18.448 1275 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 1.68 % Allowed : 22.46 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.23 (0.26), residues: 1140 helix: 1.08 (0.24), residues: 526 sheet: -0.43 (0.48), residues: 116 loop : -0.64 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 479 HIS 0.003 0.001 HIS A 362 PHE 0.031 0.002 PHE A 668 TYR 0.016 0.001 TYR A 698 ARG 0.005 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 163 average time/residue: 1.0449 time to fit residues: 185.3954 Evaluate side-chains 155 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.0670 time to fit residues: 2.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 380 ASN A 426 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9828 Z= 0.178 Angle : 0.631 10.757 13247 Z= 0.318 Chirality : 0.042 0.176 1436 Planarity : 0.004 0.061 1693 Dihedral : 3.959 18.484 1275 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 1.49 % Allowed : 23.39 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.22 (0.26), residues: 1140 helix: 1.10 (0.24), residues: 527 sheet: -0.44 (0.47), residues: 116 loop : -0.69 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.034 0.001 PHE A 668 TYR 0.022 0.001 TYR A 165 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 0.9863 time to fit residues: 165.9734 Evaluate side-chains 149 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1349 time to fit residues: 1.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0951 > 50: distance: 12 - 37: 3.297 distance: 19 - 46: 10.148 distance: 24 - 60: 10.409 distance: 29 - 37: 4.792 distance: 30 - 68: 7.898 distance: 38 - 39: 5.522 distance: 38 - 41: 3.556 distance: 39 - 40: 12.421 distance: 39 - 46: 11.884 distance: 40 - 77: 15.057 distance: 42 - 43: 3.422 distance: 43 - 44: 6.106 distance: 43 - 45: 6.978 distance: 46 - 47: 6.378 distance: 47 - 50: 6.770 distance: 48 - 49: 4.268 distance: 48 - 60: 7.744 distance: 49 - 85: 9.927 distance: 50 - 51: 5.909 distance: 51 - 52: 3.035 distance: 51 - 53: 3.215 distance: 52 - 54: 3.427 distance: 53 - 55: 3.771 distance: 53 - 56: 3.016 distance: 54 - 55: 3.148 distance: 55 - 57: 3.553 distance: 56 - 58: 3.758 distance: 57 - 59: 3.749 distance: 58 - 59: 5.216 distance: 60 - 61: 6.178 distance: 61 - 62: 14.012 distance: 61 - 64: 9.406 distance: 62 - 63: 13.154 distance: 62 - 68: 5.937 distance: 64 - 65: 5.164 distance: 65 - 66: 11.322 distance: 65 - 67: 8.988 distance: 68 - 69: 3.406 distance: 69 - 72: 3.196 distance: 70 - 71: 10.821 distance: 70 - 77: 10.008 distance: 72 - 73: 5.616 distance: 74 - 75: 4.623 distance: 75 - 76: 4.796 distance: 78 - 81: 5.382 distance: 79 - 80: 6.327 distance: 79 - 85: 17.062 distance: 85 - 86: 5.552 distance: 86 - 87: 3.399 distance: 86 - 89: 5.251 distance: 87 - 88: 8.229 distance: 87 - 94: 4.541 distance: 89 - 90: 5.298 distance: 90 - 91: 4.722 distance: 91 - 92: 8.037 distance: 95 - 98: 3.962 distance: 102 - 103: 5.535 distance: 103 - 104: 9.617 distance: 103 - 106: 11.365 distance: 104 - 105: 23.890 distance: 104 - 111: 24.831 distance: 106 - 107: 4.869 distance: 107 - 108: 4.893 distance: 108 - 109: 8.799 distance: 109 - 110: 3.409 distance: 111 - 112: 20.512 distance: 112 - 113: 8.287 distance: 113 - 114: 6.262 distance: 113 - 115: 19.473 distance: 115 - 116: 4.675 distance: 116 - 117: 6.294 distance: 117 - 118: 8.658 distance: 119 - 120: 8.665 distance: 120 - 121: 4.481 distance: 121 - 123: 3.840