Starting phenix.real_space_refine on Thu Feb 13 02:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.map" model { file = "/net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m71_30127/02_2025/6m71_30127.cif" } resolution = 2.9 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= 0.001 sd= 0.063 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 63 5.16 5 C 5507 2.51 5 N 1436 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6903 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 538 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 315 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 858 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.74, per 1000 atoms: 0.67 Number of scatterers: 8614 At special positions: 0 Unit cell: (88.56, 95.12, 117.26, 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 63 16.00 O 1608 8.00 N 1436 7.00 C 5507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.71 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 645 " distance=2.76 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 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: 50 helices and 8 sheets defined 51.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.591A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.402A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.532A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.729A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.605A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.120A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.684A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.573A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.921A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.823A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.682A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.350A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.511A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.597A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.581A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 867 removed outlier: 4.004A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.602A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.772A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.508A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.573A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.133A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.512A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.052A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.158A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 560 removed outlier: 7.004A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 189 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 155 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.918A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821 393 hydrogen bonds defined for protein. 1104 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: 2.73 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: 2765 1.34 - 1.46: 1748 1.46 - 1.58: 4196 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8805 Sorted by residual: bond pdb=" CA LEU A 931 " pdb=" C LEU A 931 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.41e-02 5.03e+03 8.83e+00 bond pdb=" N VAL A 930 " pdb=" CA VAL A 930 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.34e+00 bond pdb=" N THR A 929 " pdb=" CA THR A 929 " ideal model delta sigma weight residual 1.466 1.431 0.034 1.51e-02 4.39e+03 5.21e+00 bond pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.93e+00 bond pdb=" C PRO A 927 " pdb=" N HIS A 928 " ideal model delta sigma weight residual 1.332 1.308 0.023 1.53e-02 4.27e+03 2.36e+00 ... (remaining 8800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 11894 2.83 - 5.67: 56 5.67 - 8.50: 4 8.50 - 11.33: 1 11.33 - 14.17: 1 Bond angle restraints: 11956 Sorted by residual: angle pdb=" N VAL A 495 " pdb=" CA VAL A 495 " pdb=" C VAL A 495 " ideal model delta sigma weight residual 107.98 118.88 -10.90 1.51e+00 4.39e-01 5.21e+01 angle pdb=" N VAL A 930 " pdb=" CA VAL A 930 " pdb=" C VAL A 930 " ideal model delta sigma weight residual 109.34 123.51 -14.17 2.08e+00 2.31e-01 4.64e+01 angle pdb=" N ASN A 497 " pdb=" CA ASN A 497 " pdb=" C ASN A 497 " ideal model delta sigma weight residual 111.02 115.22 -4.20 1.25e+00 6.40e-01 1.13e+01 angle pdb=" N THR A 929 " pdb=" CA THR A 929 " pdb=" C THR A 929 " ideal model delta sigma weight residual 107.67 100.79 6.88 2.09e+00 2.29e-01 1.08e+01 angle pdb=" C THR A 929 " pdb=" CA THR A 929 " pdb=" CB THR A 929 " ideal model delta sigma weight residual 112.09 107.64 4.45 1.43e+00 4.89e-01 9.68e+00 ... (remaining 11951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4794 17.96 - 35.93: 373 35.93 - 53.89: 55 53.89 - 71.85: 12 71.85 - 89.82: 4 Dihedral angle restraints: 5238 sinusoidal: 2021 harmonic: 3217 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C VAL A 930 " pdb=" N VAL A 930 " pdb=" CA VAL A 930 " pdb=" CB VAL A 930 " ideal model delta harmonic sigma weight residual -122.00 -133.00 11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual 93.00 56.68 36.32 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1286 0.088 - 0.176: 63 0.176 - 0.264: 3 0.264 - 0.352: 1 0.352 - 0.440: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA VAL A 930 " pdb=" N VAL A 930 " pdb=" C VAL A 930 " pdb=" CB VAL A 930 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASN A 497 " pdb=" N ASN A 497 " pdb=" C ASN A 497 " pdb=" CB ASN A 497 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL A 495 " pdb=" N VAL A 495 " pdb=" C VAL A 495 " pdb=" CB VAL A 495 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1351 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 305 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ARG A 305 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 305 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS A 306 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A 232 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 339 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.022 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 69 2.55 - 3.14: 6939 3.14 - 3.73: 13228 3.73 - 4.31: 19144 4.31 - 4.90: 31839 Nonbonded interactions: 71219 Sorted by model distance: nonbonded pdb=" O VAL A 335 " pdb=" OD1 ASP A 336 " model vdw 1.966 3.040 nonbonded pdb=" O PHE A 506 " pdb=" OH TYR A 515 " model vdw 2.216 3.040 nonbonded pdb=" O PRO A 412 " pdb=" OH TYR A 546 " model vdw 2.219 3.040 nonbonded pdb=" O THR A 929 " pdb=" OG1 THR A 929 " model vdw 2.246 3.040 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.256 3.040 ... (remaining 71214 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: 2.960 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.300 Find NCS groups from input model: 0.090 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:15.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.042 8805 Z= 0.204 Angle : 0.592 14.168 11956 Z= 0.356 Chirality : 0.045 0.440 1354 Planarity : 0.004 0.046 1522 Dihedral : 13.419 89.815 3150 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -3.06 (0.22), residues: 1065 helix: -1.49 (0.20), residues: 511 sheet: -1.80 (0.41), residues: 107 loop : -2.65 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 154 HIS 0.004 0.001 HIS A 439 PHE 0.016 0.001 PHE A 652 TYR 0.018 0.001 TYR A 788 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.6852 (tpp) cc_final: 0.6638 (tpp) REVERT: C 52 MET cc_start: 0.8261 (tpp) cc_final: 0.7208 (tmm) REVERT: D 101 ASP cc_start: 0.8004 (p0) cc_final: 0.7582 (p0) REVERT: B 156 ILE cc_start: 0.7742 (pt) cc_final: 0.7531 (pt) REVERT: B 168 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6509 (mp-120) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 1.1313 time to fit residues: 206.1946 Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 360 ASN A 414 ASN A 572 HIS A 599 HIS A 613 HIS A 773 GLN C 18 GLN C 36 HIS D 100 ASN D 105 ASN B 118 ASN B 140 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118373 restraints weight = 13713.267| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.05 r_work: 0.3508 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8805 Z= 0.180 Angle : 0.531 7.263 11956 Z= 0.285 Chirality : 0.042 0.211 1354 Planarity : 0.004 0.038 1522 Dihedral : 4.444 22.020 1176 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.22 % Allowed : 12.38 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.43 (0.24), residues: 1065 helix: 0.11 (0.23), residues: 503 sheet: -1.61 (0.43), residues: 102 loop : -1.98 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.005 0.001 HIS A 725 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.002 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.927 Fit side-chains REVERT: A 333 ILE cc_start: 0.8151 (pt) cc_final: 0.7911 (pt) REVERT: A 372 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 705 ASN cc_start: 0.8452 (m110) cc_final: 0.8243 (m110) REVERT: C 3 MET cc_start: 0.6650 (tpp) cc_final: 0.6429 (tpp) REVERT: C 47 GLU cc_start: 0.7009 (mp0) cc_final: 0.6729 (mp0) REVERT: D 101 ASP cc_start: 0.8182 (p0) cc_final: 0.7721 (p0) outliers start: 21 outliers final: 7 residues processed: 150 average time/residue: 1.0007 time to fit residues: 162.2172 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 414 ASN A 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113759 restraints weight = 13889.530| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.08 r_work: 0.3440 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8805 Z= 0.358 Angle : 0.606 7.384 11956 Z= 0.325 Chirality : 0.046 0.224 1354 Planarity : 0.004 0.039 1522 Dihedral : 4.817 29.513 1176 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.39 % Allowed : 14.39 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.23 (0.24), residues: 1065 helix: 0.29 (0.23), residues: 498 sheet: -1.92 (0.48), residues: 91 loop : -1.78 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 154 HIS 0.008 0.001 HIS A 650 PHE 0.020 0.002 PHE A 741 TYR 0.019 0.002 TYR A 770 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 705 ASN cc_start: 0.8487 (m110) cc_final: 0.8243 (m110) REVERT: A 818 MET cc_start: 0.6835 (ptt) cc_final: 0.6288 (pmt) REVERT: A 882 HIS cc_start: 0.7461 (m-70) cc_final: 0.7123 (m170) REVERT: C 3 MET cc_start: 0.6989 (tpp) cc_final: 0.6739 (tpp) REVERT: C 47 GLU cc_start: 0.6998 (mp0) cc_final: 0.6741 (mp0) REVERT: D 101 ASP cc_start: 0.8099 (p0) cc_final: 0.7682 (p0) outliers start: 32 outliers final: 17 residues processed: 155 average time/residue: 0.9477 time to fit residues: 159.4554 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 106 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 541 GLN A 650 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.118619 restraints weight = 13743.418| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.08 r_work: 0.3511 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8805 Z= 0.158 Angle : 0.509 7.277 11956 Z= 0.272 Chirality : 0.041 0.155 1354 Planarity : 0.003 0.037 1522 Dihedral : 4.352 21.611 1176 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.75 % Allowed : 15.34 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.50 (0.25), residues: 1065 helix: 0.82 (0.24), residues: 500 sheet: -1.29 (0.48), residues: 96 loop : -1.37 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.005 0.001 HIS A 613 PHE 0.015 0.001 PHE A 368 TYR 0.019 0.001 TYR A 420 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.122 Fit side-chains REVERT: A 372 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 705 ASN cc_start: 0.8417 (m110) cc_final: 0.8142 (m110) REVERT: A 818 MET cc_start: 0.6679 (ptt) cc_final: 0.6084 (pmt) REVERT: A 882 HIS cc_start: 0.7334 (m-70) cc_final: 0.6993 (m170) REVERT: C 3 MET cc_start: 0.6664 (tpp) cc_final: 0.6322 (tpp) REVERT: D 101 ASP cc_start: 0.8107 (p0) cc_final: 0.7717 (p0) REVERT: B 96 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6764 (mtp180) outliers start: 26 outliers final: 12 residues processed: 157 average time/residue: 1.0035 time to fit residues: 170.9745 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114608 restraints weight = 13757.312| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.07 r_work: 0.3437 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8805 Z= 0.314 Angle : 0.581 7.206 11956 Z= 0.310 Chirality : 0.044 0.154 1354 Planarity : 0.004 0.044 1522 Dihedral : 4.633 27.386 1176 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.81 % Allowed : 16.08 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.66 (0.25), residues: 1065 helix: 0.66 (0.24), residues: 499 sheet: -1.43 (0.50), residues: 91 loop : -1.40 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 154 HIS 0.005 0.001 HIS A 725 PHE 0.019 0.002 PHE A 741 TYR 0.023 0.002 TYR A 420 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8201 (tp) cc_final: 0.7927 (tp) REVERT: A 372 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 705 ASN cc_start: 0.8449 (m110) cc_final: 0.8204 (m110) REVERT: A 818 MET cc_start: 0.6778 (ptt) cc_final: 0.6216 (pmt) REVERT: A 882 HIS cc_start: 0.7452 (m-70) cc_final: 0.7121 (m170) REVERT: C 3 MET cc_start: 0.6911 (tpp) cc_final: 0.6688 (tpp) REVERT: D 101 ASP cc_start: 0.8144 (p0) cc_final: 0.7758 (p0) outliers start: 36 outliers final: 21 residues processed: 157 average time/residue: 0.9829 time to fit residues: 167.6242 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 95 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118721 restraints weight = 13641.582| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.08 r_work: 0.3511 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8805 Z= 0.166 Angle : 0.528 7.515 11956 Z= 0.279 Chirality : 0.041 0.158 1354 Planarity : 0.003 0.040 1522 Dihedral : 4.268 21.142 1176 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 17.46 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1065 helix: 0.96 (0.24), residues: 503 sheet: -1.02 (0.51), residues: 96 loop : -1.08 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.023 0.001 TYR A 420 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.021 Fit side-chains REVERT: A 113 HIS cc_start: 0.6844 (m-70) cc_final: 0.6526 (m-70) REVERT: A 241 LEU cc_start: 0.8049 (tp) cc_final: 0.7761 (tp) REVERT: A 340 PHE cc_start: 0.7376 (m-80) cc_final: 0.7094 (m-80) REVERT: A 705 ASN cc_start: 0.8381 (m110) cc_final: 0.8074 (m110) REVERT: A 818 MET cc_start: 0.6706 (ptt) cc_final: 0.6105 (pmt) REVERT: A 882 HIS cc_start: 0.7350 (m-70) cc_final: 0.7001 (m170) REVERT: D 101 ASP cc_start: 0.8122 (p0) cc_final: 0.7779 (p0) REVERT: B 96 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6780 (mtp180) REVERT: B 174 MET cc_start: 0.7659 (tmm) cc_final: 0.7124 (tpp) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.9404 time to fit residues: 157.2245 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.136975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118346 restraints weight = 13756.216| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.08 r_work: 0.3488 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8805 Z= 0.229 Angle : 0.569 9.315 11956 Z= 0.301 Chirality : 0.043 0.153 1354 Planarity : 0.004 0.049 1522 Dihedral : 4.337 24.047 1176 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.07 % Allowed : 18.41 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1065 helix: 0.85 (0.24), residues: 509 sheet: -0.77 (0.53), residues: 87 loop : -1.10 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 PHE 0.017 0.002 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.007 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.942 Fit side-chains REVERT: A 241 LEU cc_start: 0.8060 (tp) cc_final: 0.7797 (tp) REVERT: A 340 PHE cc_start: 0.7431 (m-80) cc_final: 0.7161 (m-80) REVERT: A 705 ASN cc_start: 0.8352 (m110) cc_final: 0.8065 (m110) REVERT: A 818 MET cc_start: 0.6764 (ptt) cc_final: 0.6204 (pmt) REVERT: A 882 HIS cc_start: 0.7323 (m-70) cc_final: 0.6998 (m170) REVERT: D 101 ASP cc_start: 0.8114 (p0) cc_final: 0.7795 (p0) REVERT: B 96 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6815 (mtp180) REVERT: B 154 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.7459 (m100) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.9116 time to fit residues: 155.7309 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 81 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119677 restraints weight = 13825.077| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.07 r_work: 0.3526 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8805 Z= 0.156 Angle : 0.545 7.880 11956 Z= 0.286 Chirality : 0.042 0.155 1354 Planarity : 0.003 0.050 1522 Dihedral : 4.141 20.488 1176 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 19.05 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.12 (0.26), residues: 1065 helix: 1.17 (0.24), residues: 496 sheet: -0.54 (0.50), residues: 97 loop : -0.94 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS A 613 PHE 0.015 0.001 PHE A 741 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.222 Fit side-chains REVERT: A 241 LEU cc_start: 0.7999 (tp) cc_final: 0.7712 (tp) REVERT: A 340 PHE cc_start: 0.7267 (m-80) cc_final: 0.7063 (m-80) REVERT: A 705 ASN cc_start: 0.8339 (m110) cc_final: 0.8035 (m110) REVERT: A 818 MET cc_start: 0.6671 (ptt) cc_final: 0.6092 (pmt) REVERT: A 882 HIS cc_start: 0.7304 (m-70) cc_final: 0.7012 (m170) REVERT: D 101 ASP cc_start: 0.8111 (p0) cc_final: 0.7796 (p0) REVERT: B 96 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6780 (mtp180) REVERT: B 154 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.6550 (m100) REVERT: B 174 MET cc_start: 0.7644 (tmm) cc_final: 0.7145 (tpp) outliers start: 22 outliers final: 11 residues processed: 147 average time/residue: 0.9049 time to fit residues: 146.4251 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117409 restraints weight = 13795.554| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.06 r_work: 0.3488 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8805 Z= 0.240 Angle : 0.584 9.069 11956 Z= 0.308 Chirality : 0.043 0.157 1354 Planarity : 0.004 0.058 1522 Dihedral : 4.297 24.196 1176 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.22 % Allowed : 19.79 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.10 (0.26), residues: 1065 helix: 0.89 (0.23), residues: 511 sheet: -0.69 (0.54), residues: 87 loop : -0.97 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 PHE 0.017 0.002 PHE A 741 TYR 0.027 0.001 TYR A 420 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.935 Fit side-chains REVERT: A 241 LEU cc_start: 0.8113 (tp) cc_final: 0.7840 (tp) REVERT: A 372 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 705 ASN cc_start: 0.8342 (m110) cc_final: 0.8065 (m110) REVERT: A 818 MET cc_start: 0.6749 (ptt) cc_final: 0.6205 (pmt) REVERT: A 882 HIS cc_start: 0.7319 (m-70) cc_final: 0.7015 (m170) REVERT: C 15 SER cc_start: 0.8519 (t) cc_final: 0.8299 (m) REVERT: D 101 ASP cc_start: 0.8121 (p0) cc_final: 0.7813 (p0) REVERT: B 96 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6799 (mtp180) REVERT: B 154 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7453 (m100) REVERT: B 174 MET cc_start: 0.7634 (tmm) cc_final: 0.7124 (tpp) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.9326 time to fit residues: 145.1916 Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119915 restraints weight = 13753.682| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.07 r_work: 0.3530 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8805 Z= 0.171 Angle : 0.574 9.434 11956 Z= 0.300 Chirality : 0.042 0.159 1354 Planarity : 0.004 0.059 1522 Dihedral : 4.157 20.624 1176 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.80 % Allowed : 20.74 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1065 helix: 1.06 (0.23), residues: 510 sheet: -0.79 (0.50), residues: 104 loop : -0.87 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.006 0.001 HIS A 613 PHE 0.015 0.001 PHE A 741 TYR 0.024 0.001 TYR A 420 ARG 0.005 0.000 ARG C 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.834 Fit side-chains REVERT: A 241 LEU cc_start: 0.8020 (tp) cc_final: 0.7725 (tp) REVERT: A 372 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 705 ASN cc_start: 0.8364 (m110) cc_final: 0.8046 (m110) REVERT: A 818 MET cc_start: 0.6651 (ptt) cc_final: 0.6087 (pmt) REVERT: A 882 HIS cc_start: 0.7311 (m-70) cc_final: 0.7018 (m170) REVERT: D 87 MET cc_start: 0.7963 (tmm) cc_final: 0.6514 (ttp) REVERT: D 101 ASP cc_start: 0.8104 (p0) cc_final: 0.7791 (p0) REVERT: B 87 MET cc_start: 0.8246 (mtp) cc_final: 0.8045 (mtp) REVERT: B 96 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6787 (mtp180) REVERT: B 154 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.6399 (m100) REVERT: B 174 MET cc_start: 0.7595 (tmm) cc_final: 0.7276 (tpp) outliers start: 17 outliers final: 10 residues processed: 139 average time/residue: 0.9536 time to fit residues: 144.3596 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120102 restraints weight = 13866.511| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.06 r_work: 0.3531 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8805 Z= 0.174 Angle : 0.573 9.357 11956 Z= 0.297 Chirality : 0.042 0.171 1354 Planarity : 0.004 0.058 1522 Dihedral : 4.069 20.459 1176 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 21.16 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.15 (0.26), residues: 1065 helix: 1.14 (0.23), residues: 510 sheet: -0.72 (0.51), residues: 104 loop : -0.85 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.024 0.001 TYR A 420 ARG 0.005 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5864.57 seconds wall clock time: 104 minutes 12.73 seconds (6252.73 seconds total)