Starting phenix.real_space_refine on Fri Oct 11 02:20:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/10_2024/8dp0_27627.cif" } resolution = 2.96 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= -0.017 sd= 0.061 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 43 5.16 5 C 5699 2.51 5 N 1529 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7964 Classifications: {'peptide': 979} Link IDs: {'PTRANS': 46, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 930 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Time building chain proxies: 5.71, per 1000 atoms: 0.64 Number of scatterers: 8894 At special positions: 0 Unit cell: (87.98, 92.96, 107.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1623 8.00 N 1529 7.00 C 5699 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 46.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.119A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.540A pdb=" N GLN A 117 " --> pdb=" O GLN A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.097A pdb=" N GLY A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 332 " --> pdb=" O CYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 6.568A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.721A pdb=" N ARG A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 688 through 706 Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.503A pdb=" N PHE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 removed outlier: 3.641A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 798 through 801 Processing helix chain 'A' and resid 838 through 857 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.987A pdb=" N THR A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 915 removed outlier: 4.542A pdb=" N ASN A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 964 through 976 removed outlier: 3.820A pdb=" N ILE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.699A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.609A pdb=" N MET A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1055 removed outlier: 4.315A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1078 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.949A pdb=" N TRP B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 3.835A pdb=" N GLU A 55 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235 removed outlier: 7.145A pdb=" N PHE A 221 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 305 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 223 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 307 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS A 225 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.058A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.421A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 412 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 365 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 519 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 478 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 398 removed outlier: 6.734A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 429 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 465 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1200 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: 3.31 Time building geometry restraints manager: 2.58 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: 2890 1.34 - 1.46: 1560 1.46 - 1.57: 4590 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 9105 Sorted by residual: bond pdb=" C ARG A 614 " pdb=" N GLU A 615 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.29e-02 6.01e+03 1.75e+00 bond pdb=" C ALA B 98 " pdb=" O ALA B 98 " ideal model delta sigma weight residual 1.243 1.234 0.010 9.50e-03 1.11e+04 1.07e+00 bond pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 1.469 1.481 -0.013 1.28e-02 6.10e+03 9.90e-01 bond pdb=" CB ILE A 643 " pdb=" CG2 ILE A 643 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.20e-01 bond pdb=" N GLY A 996 " pdb=" CA GLY A 996 " ideal model delta sigma weight residual 1.449 1.437 0.012 1.45e-02 4.76e+03 6.78e-01 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12135 1.56 - 3.13: 176 3.13 - 4.69: 21 4.69 - 6.25: 6 6.25 - 7.82: 3 Bond angle restraints: 12341 Sorted by residual: angle pdb=" C ALA B 98 " pdb=" CA ALA B 98 " pdb=" CB ALA B 98 " ideal model delta sigma weight residual 117.23 109.41 7.82 1.36e+00 5.41e-01 3.30e+01 angle pdb=" CA ALA B 98 " pdb=" C ALA B 98 " pdb=" N GLY B 99 " ideal model delta sigma weight residual 119.98 116.67 3.31 8.50e-01 1.38e+00 1.52e+01 angle pdb=" N VAL A 67 " pdb=" CA VAL A 67 " pdb=" C VAL A 67 " ideal model delta sigma weight residual 111.77 108.49 3.28 1.04e+00 9.25e-01 9.96e+00 angle pdb=" N ALA B 98 " pdb=" CA ALA B 98 " pdb=" C ALA B 98 " ideal model delta sigma weight residual 108.67 113.69 -5.02 1.67e+00 3.59e-01 9.05e+00 angle pdb=" N VAL A 326 " pdb=" CA VAL A 326 " pdb=" CB VAL A 326 " ideal model delta sigma weight residual 112.21 109.01 3.20 1.10e+00 8.26e-01 8.49e+00 ... (remaining 12336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4870 15.95 - 31.90: 456 31.90 - 47.85: 91 47.85 - 63.80: 22 63.80 - 79.75: 9 Dihedral angle restraints: 5448 sinusoidal: 2234 harmonic: 3214 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" CB ASP B 61 " pdb=" CG ASP B 61 " pdb=" OD1 ASP B 61 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASN B 96 " pdb=" C ASN B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N GLN A 69 " pdb=" CA GLN A 69 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 921 0.033 - 0.065: 302 0.065 - 0.098: 92 0.098 - 0.131: 48 0.131 - 0.164: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA THR A 182 " pdb=" N THR A 182 " pdb=" C THR A 182 " pdb=" CB THR A 182 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE A 643 " pdb=" CA ILE A 643 " pdb=" CG1 ILE A 643 " pdb=" CG2 ILE A 643 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 368 " pdb=" N ILE A 368 " pdb=" C ILE A 368 " pdb=" CB ILE A 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1363 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 547 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A 548 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 988 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 371 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.023 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 979 2.75 - 3.29: 8630 3.29 - 3.83: 14731 3.83 - 4.36: 17801 4.36 - 4.90: 30811 Nonbonded interactions: 72952 Sorted by model distance: nonbonded pdb=" OH TYR A1017 " pdb=" O ALA A1054 " model vdw 2.213 3.040 nonbonded pdb=" O TRP A 617 " pdb=" OG SER A 620 " model vdw 2.221 3.040 nonbonded pdb=" OE1 GLN A 705 " pdb=" OG SER A 871 " model vdw 2.268 3.040 nonbonded pdb=" O MET A1033 " pdb=" OG1 THR A1037 " model vdw 2.270 3.040 nonbonded pdb=" OE2 GLU A 384 " pdb=" NE2 GLN A 396 " model vdw 2.280 3.120 ... (remaining 72947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.950 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.480 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.002 0.030 9105 Z= 0.162 Angle : 0.500 7.818 12341 Z= 0.278 Chirality : 0.040 0.164 1366 Planarity : 0.004 0.070 1577 Dihedral : 13.313 79.755 3366 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1.09 (0.26), residues: 1088 helix: 1.71 (0.25), residues: 452 sheet: 0.23 (0.36), residues: 186 loop : 0.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 125 HIS 0.006 0.001 HIS A1023 PHE 0.011 0.001 PHE A 473 TYR 0.016 0.001 TYR A 110 ARG 0.007 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 1.1046 time to fit residues: 266.9708 Evaluate side-chains 112 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0470 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 959 ASN A1083 GLN B 32 ASN B 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9105 Z= 0.325 Angle : 0.718 9.657 12341 Z= 0.373 Chirality : 0.047 0.178 1366 Planarity : 0.005 0.062 1577 Dihedral : 4.511 17.315 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.40 % Allowed : 10.75 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1088 helix: 1.13 (0.24), residues: 458 sheet: -0.14 (0.34), residues: 177 loop : -0.23 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 812 HIS 0.007 0.001 HIS B 50 PHE 0.014 0.002 PHE A 290 TYR 0.022 0.002 TYR A1067 ARG 0.007 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.057 Fit side-chains outliers start: 43 outliers final: 10 residues processed: 133 average time/residue: 1.1739 time to fit residues: 168.2906 Evaluate side-chains 84 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 386 ASN A 432 GLN A 735 GLN A 951 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9105 Z= 0.207 Angle : 0.546 10.271 12341 Z= 0.275 Chirality : 0.042 0.192 1366 Planarity : 0.004 0.060 1577 Dihedral : 3.812 16.064 1185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 14.84 % Favored : 82.60 % 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: 0.97 (0.25), residues: 1088 helix: 1.69 (0.24), residues: 459 sheet: 0.17 (0.36), residues: 186 loop : -0.17 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 812 HIS 0.006 0.001 HIS B 50 PHE 0.013 0.001 PHE A 578 TYR 0.012 0.001 TYR A 935 ARG 0.005 0.001 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 75 time to evaluate : 1.057 Fit side-chains outliers start: 25 outliers final: 8 residues processed: 95 average time/residue: 1.0693 time to fit residues: 110.6455 Evaluate side-chains 79 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9105 Z= 0.188 Angle : 0.526 10.835 12341 Z= 0.263 Chirality : 0.041 0.198 1366 Planarity : 0.004 0.060 1577 Dihedral : 3.644 15.250 1185 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.66 % Allowed : 15.25 % Favored : 82.09 % 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: 1.09 (0.26), residues: 1088 helix: 1.83 (0.24), residues: 459 sheet: 0.06 (0.35), residues: 192 loop : -0.07 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 29 TYR 0.013 0.001 TYR A1067 ARG 0.006 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.966 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 97 average time/residue: 1.0060 time to fit residues: 106.5289 Evaluate side-chains 77 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 961 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1041 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 9105 Z= 0.299 Angle : 0.577 9.428 12341 Z= 0.291 Chirality : 0.043 0.238 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.919 16.027 1185 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.76 % Allowed : 16.48 % Favored : 80.76 % 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: 0.94 (0.25), residues: 1088 helix: 1.73 (0.24), residues: 460 sheet: -0.02 (0.35), residues: 190 loop : -0.18 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.013 0.001 PHE B 113 TYR 0.014 0.001 TYR A1067 ARG 0.006 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.087 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 89 average time/residue: 1.0088 time to fit residues: 98.2153 Evaluate side-chains 72 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9105 Z= 0.227 Angle : 0.536 10.455 12341 Z= 0.269 Chirality : 0.042 0.214 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.785 15.220 1185 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.76 % Allowed : 17.50 % Favored : 79.73 % 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: 1.05 (0.25), residues: 1088 helix: 1.84 (0.24), residues: 458 sheet: -0.05 (0.36), residues: 180 loop : -0.09 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 PHE 0.011 0.001 PHE A 382 TYR 0.012 0.001 TYR A1067 ARG 0.004 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.112 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 88 average time/residue: 0.8819 time to fit residues: 86.1941 Evaluate side-chains 71 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0370 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9105 Z= 0.163 Angle : 0.525 11.266 12341 Z= 0.261 Chirality : 0.041 0.206 1366 Planarity : 0.004 0.061 1577 Dihedral : 3.635 14.677 1185 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.25 % Allowed : 18.94 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1088 helix: 1.88 (0.24), residues: 459 sheet: 0.05 (0.35), residues: 192 loop : -0.08 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.010 0.001 PHE B 29 TYR 0.011 0.001 TYR A 720 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.972 Fit side-chains REVERT: A 1039 MET cc_start: 0.8274 (mmp) cc_final: 0.8027 (mmp) outliers start: 22 outliers final: 11 residues processed: 79 average time/residue: 0.8802 time to fit residues: 76.9377 Evaluate side-chains 68 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.7823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9105 Z= 0.276 Angle : 0.553 9.352 12341 Z= 0.276 Chirality : 0.042 0.220 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.748 15.305 1185 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 18.83 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1088 helix: 1.84 (0.24), residues: 458 sheet: 0.02 (0.35), residues: 192 loop : -0.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 PHE 0.012 0.001 PHE A 382 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.997 Fit side-chains REVERT: A 1039 MET cc_start: 0.8349 (mmp) cc_final: 0.8137 (mmp) outliers start: 23 outliers final: 14 residues processed: 83 average time/residue: 1.0335 time to fit residues: 93.7606 Evaluate side-chains 70 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 88 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9105 Z= 0.179 Angle : 0.542 11.436 12341 Z= 0.269 Chirality : 0.041 0.204 1366 Planarity : 0.004 0.066 1577 Dihedral : 3.651 15.143 1185 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 20.06 % Favored : 78.30 % 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: 1.16 (0.26), residues: 1088 helix: 1.94 (0.24), residues: 459 sheet: 0.06 (0.35), residues: 192 loop : -0.09 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE A 961 TYR 0.011 0.001 TYR A1067 ARG 0.027 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.080 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.9453 time to fit residues: 76.0544 Evaluate side-chains 70 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-dev-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-dev-5477/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-dev-5477/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-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-dev-5477/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-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-dev-5477/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-dev-5477/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-dev-5477/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-dev-5477/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: 66.0872 > 50: distance: 84 - 109: 13.216 distance: 87 - 93: 24.246 distance: 88 - 117: 12.616 distance: 93 - 94: 41.347 distance: 93 - 99: 41.341 distance: 94 - 95: 34.469 distance: 94 - 97: 34.965 distance: 95 - 96: 35.287 distance: 95 - 100: 41.933 distance: 96 - 128: 22.785 distance: 97 - 98: 33.370 distance: 98 - 99: 32.280 distance: 100 - 101: 47.607 distance: 101 - 102: 47.749 distance: 101 - 104: 53.615 distance: 102 - 103: 31.791 distance: 102 - 109: 30.313 distance: 103 - 134: 10.149 distance: 104 - 105: 29.780 distance: 105 - 106: 9.110 distance: 106 - 107: 13.297 distance: 107 - 108: 15.939 distance: 109 - 110: 8.320 distance: 110 - 111: 8.392 distance: 110 - 113: 9.502 distance: 111 - 112: 18.311 distance: 111 - 117: 21.064 distance: 113 - 114: 32.801 distance: 114 - 115: 32.899 distance: 114 - 116: 26.360 distance: 117 - 118: 16.521 distance: 118 - 119: 27.292 distance: 118 - 121: 28.012 distance: 119 - 120: 33.821 distance: 119 - 128: 43.621 distance: 121 - 122: 36.740 distance: 122 - 123: 10.109 distance: 122 - 124: 24.068 distance: 123 - 125: 21.594 distance: 124 - 126: 48.185 distance: 125 - 127: 18.655 distance: 126 - 127: 23.033 distance: 128 - 129: 17.773 distance: 129 - 130: 35.128 distance: 129 - 132: 25.996 distance: 130 - 131: 10.076 distance: 130 - 134: 23.131 distance: 132 - 133: 20.809 distance: 134 - 135: 27.183 distance: 135 - 136: 39.961 distance: 135 - 138: 19.103 distance: 136 - 137: 24.204 distance: 136 - 140: 12.097 distance: 138 - 139: 51.254 distance: 140 - 141: 9.800 distance: 141 - 142: 25.991 distance: 141 - 144: 23.146 distance: 142 - 143: 15.228 distance: 142 - 147: 36.821 distance: 144 - 145: 25.775 distance: 144 - 146: 32.393 distance: 147 - 148: 19.168 distance: 148 - 149: 34.811 distance: 148 - 151: 26.784 distance: 149 - 150: 35.161 distance: 149 - 156: 48.958 distance: 151 - 152: 45.508 distance: 152 - 153: 36.000 distance: 153 - 154: 23.116 distance: 154 - 155: 13.979 distance: 156 - 157: 43.006 distance: 157 - 158: 30.642 distance: 157 - 160: 35.971 distance: 158 - 159: 51.579 distance: 158 - 170: 41.025 distance: 160 - 161: 10.188 distance: 161 - 162: 40.902 distance: 161 - 163: 35.121 distance: 162 - 164: 24.749 distance: 163 - 165: 24.061 distance: 163 - 166: 20.302 distance: 164 - 165: 21.296 distance: 165 - 167: 14.054 distance: 166 - 168: 8.856 distance: 167 - 169: 8.920 distance: 168 - 169: 10.395 distance: 170 - 171: 45.576 distance: 171 - 172: 24.920 distance: 172 - 173: 43.899 distance: 172 - 174: 22.360