Starting phenix.real_space_refine on Thu Mar 13 03:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m71_30127/03_2025/6m71_30127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m71_30127/03_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_30127/03_2025/6m71_30127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2025/6m71_30127.map" model { file = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2025/6m71_30127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.15, per 1000 atoms: 0.60 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 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: 1.08 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: 2.86 Time building geometry restraints manager: 2.60 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: 2.290 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- 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 : 0.890 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: 1.1261 time to fit residues: 205.0430 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 : 0.951 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118321 restraints weight = 13713.269| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.06 r_work: 0.3508 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- 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 : 0.946 Fit side-chains REVERT: A 333 ILE cc_start: 0.8161 (pt) cc_final: 0.7919 (pt) REVERT: A 372 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 705 ASN cc_start: 0.8449 (m110) cc_final: 0.8242 (m110) REVERT: C 3 MET cc_start: 0.6645 (tpp) cc_final: 0.6426 (tpp) REVERT: C 47 GLU cc_start: 0.7011 (mp0) cc_final: 0.6731 (mp0) REVERT: D 101 ASP cc_start: 0.8186 (p0) cc_final: 0.7728 (p0) outliers start: 21 outliers final: 7 residues processed: 150 average time/residue: 0.9930 time to fit residues: 161.4085 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 : 0.960 ------------------------------------------------------------------------------- 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: 0.1980 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 103 optimal weight: 0.0470 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.137053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118205 restraints weight = 13772.872| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.08 r_work: 0.3501 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8805 Z= 0.196 Angle : 0.522 7.154 11956 Z= 0.278 Chirality : 0.042 0.217 1354 Planarity : 0.003 0.035 1522 Dihedral : 4.320 22.786 1176 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 14.39 % Favored : 83.17 % 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: -0.71 (0.25), residues: 1065 helix: 0.70 (0.24), residues: 500 sheet: -1.47 (0.46), residues: 91 loop : -1.54 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.004 0.001 HIS A 650 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 420 ARG 0.002 0.000 ARG B 96 *********************** 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 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ILE cc_start: 0.8166 (pt) cc_final: 0.7938 (pt) REVERT: A 370 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 372 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7918 (mp) REVERT: A 705 ASN cc_start: 0.8449 (m110) cc_final: 0.8190 (m110) REVERT: A 882 HIS cc_start: 0.7310 (m-70) cc_final: 0.7002 (m170) REVERT: C 3 MET cc_start: 0.6623 (tpp) cc_final: 0.6329 (tpp) REVERT: C 47 GLU cc_start: 0.6946 (mp0) cc_final: 0.6723 (mp0) REVERT: D 101 ASP cc_start: 0.8164 (p0) cc_final: 0.7710 (p0) REVERT: B 82 LYS cc_start: 0.8024 (tptp) cc_final: 0.7790 (tppt) outliers start: 23 outliers final: 13 residues processed: 156 average time/residue: 0.9695 time to fit residues: 164.6089 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 658 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER 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: 0.7980 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.0170 chunk 63 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119832 restraints weight = 13717.969| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.07 r_work: 0.3526 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8805 Z= 0.158 Angle : 0.497 6.982 11956 Z= 0.264 Chirality : 0.041 0.154 1354 Planarity : 0.003 0.034 1522 Dihedral : 4.157 20.415 1176 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.65 % Allowed : 15.13 % 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: -0.28 (0.26), residues: 1065 helix: 1.00 (0.24), residues: 499 sheet: -1.02 (0.45), residues: 106 loop : -1.28 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.008 0.001 HIS A 613 PHE 0.015 0.001 PHE A 368 TYR 0.018 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 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.6753 (m-70) cc_final: 0.6465 (m-70) REVERT: A 372 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 705 ASN cc_start: 0.8353 (m110) cc_final: 0.8058 (m110) REVERT: A 882 HIS cc_start: 0.7314 (m-70) cc_final: 0.7037 (m170) REVERT: C 3 MET cc_start: 0.6576 (tpp) cc_final: 0.6261 (tpp) REVERT: C 5 ASP cc_start: 0.6110 (OUTLIER) cc_final: 0.5866 (t0) REVERT: D 101 ASP cc_start: 0.8116 (p0) cc_final: 0.7720 (p0) REVERT: B 154 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.6425 (m100) REVERT: B 174 MET cc_start: 0.7720 (tmm) cc_final: 0.7153 (tpp) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 0.9823 time to fit residues: 160.5217 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 658 GLU Chi-restraints excluded: chain A residue 662 VAL 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 C residue 5 ASP Chi-restraints excluded: chain B residue 154 TRP 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: 0.0980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118673 restraints weight = 13641.876| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.08 r_work: 0.3492 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8805 Z= 0.190 Angle : 0.518 6.884 11956 Z= 0.275 Chirality : 0.041 0.157 1354 Planarity : 0.003 0.036 1522 Dihedral : 4.171 22.285 1176 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 16.51 % Favored : 80.95 % 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: 1.01 (0.24), residues: 501 sheet: -0.94 (0.50), residues: 96 loop : -1.06 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS A 725 PHE 0.016 0.001 PHE A 741 TYR 0.018 0.001 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 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.6747 (m-70) cc_final: 0.6447 (m-70) REVERT: A 372 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 705 ASN cc_start: 0.8397 (m110) cc_final: 0.8105 (m110) REVERT: A 882 HIS cc_start: 0.7305 (m-70) cc_final: 0.7028 (m170) REVERT: C 3 MET cc_start: 0.6745 (tpp) cc_final: 0.6431 (tpp) REVERT: D 101 ASP cc_start: 0.8118 (p0) cc_final: 0.7753 (p0) REVERT: B 154 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.6878 (m100) REVERT: B 174 MET cc_start: 0.7675 (tmm) cc_final: 0.7143 (tpp) outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 0.9623 time to fit residues: 156.1363 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU 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 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 658 GLU 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 85 SER Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.138661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119947 restraints weight = 13629.942| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.07 r_work: 0.3530 rms_B_bonded: 2.57 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: 0.7932 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8805 Z= 0.166 Angle : 0.516 7.583 11956 Z= 0.273 Chirality : 0.041 0.157 1354 Planarity : 0.003 0.034 1522 Dihedral : 4.059 20.632 1176 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.17 % Allowed : 16.83 % Favored : 80.00 % 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: 0.08 (0.26), residues: 1065 helix: 1.15 (0.24), residues: 501 sheet: -0.71 (0.48), residues: 106 loop : -0.96 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS A 725 PHE 0.015 0.001 PHE A 741 TYR 0.023 0.001 TYR A 420 ARG 0.003 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 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 113 HIS cc_start: 0.6697 (m-70) cc_final: 0.6395 (m-70) REVERT: A 543 ASN cc_start: 0.8118 (m-40) cc_final: 0.7890 (m-40) REVERT: A 705 ASN cc_start: 0.8354 (m110) cc_final: 0.8053 (m110) REVERT: A 882 HIS cc_start: 0.7290 (m-70) cc_final: 0.7018 (m170) REVERT: C 3 MET cc_start: 0.6697 (tpp) cc_final: 0.6341 (tpp) REVERT: D 101 ASP cc_start: 0.8165 (p0) cc_final: 0.7834 (p0) REVERT: B 154 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.6532 (m100) REVERT: B 174 MET cc_start: 0.7671 (tmm) cc_final: 0.7179 (tpp) outliers start: 30 outliers final: 18 residues processed: 152 average time/residue: 1.0083 time to fit residues: 166.0329 Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU 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 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 658 GLU 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 154 TRP Chi-restraints excluded: chain B residue 160 VAL 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: 9.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119544 restraints weight = 13745.742| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.07 r_work: 0.3526 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2276 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= 0.180 Angle : 0.534 7.361 11956 Z= 0.281 Chirality : 0.042 0.153 1354 Planarity : 0.003 0.054 1522 Dihedral : 4.066 21.050 1176 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 17.99 % Favored : 79.05 % 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: 0.17 (0.26), residues: 1065 helix: 1.21 (0.24), residues: 501 sheet: -0.73 (0.49), residues: 106 loop : -0.87 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS A 725 PHE 0.016 0.001 PHE A 741 TYR 0.020 0.001 TYR A 420 ARG 0.009 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 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 705 ASN cc_start: 0.8352 (m110) cc_final: 0.8052 (m110) REVERT: A 882 HIS cc_start: 0.7294 (m-70) cc_final: 0.7006 (m170) REVERT: C 3 MET cc_start: 0.6727 (tpp) cc_final: 0.6359 (tpp) REVERT: D 101 ASP cc_start: 0.8172 (p0) cc_final: 0.7866 (p0) REVERT: B 154 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.6427 (m100) REVERT: B 174 MET cc_start: 0.7656 (tmm) cc_final: 0.7168 (tpp) outliers start: 28 outliers final: 16 residues processed: 148 average time/residue: 0.9129 time to fit residues: 147.0839 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU 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 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 658 GLU 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 85 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116296 restraints weight = 13902.991| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.07 r_work: 0.3472 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8805 Z= 0.283 Angle : 0.584 7.569 11956 Z= 0.309 Chirality : 0.044 0.154 1354 Planarity : 0.004 0.052 1522 Dihedral : 4.392 26.223 1176 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.96 % Allowed : 18.20 % Favored : 78.84 % 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: 0.82 (0.23), residues: 515 sheet: -0.71 (0.54), residues: 87 loop : -0.98 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 154 HIS 0.004 0.001 HIS A 725 PHE 0.018 0.002 PHE A 741 TYR 0.025 0.002 TYR A 420 ARG 0.007 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 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 705 ASN cc_start: 0.8391 (m110) cc_final: 0.8118 (m110) REVERT: A 882 HIS cc_start: 0.7312 (m-70) cc_final: 0.6994 (m170) REVERT: C 3 MET cc_start: 0.6908 (tpp) cc_final: 0.6503 (tpp) REVERT: D 101 ASP cc_start: 0.8127 (p0) cc_final: 0.7814 (p0) REVERT: B 154 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7563 (m100) REVERT: B 174 MET cc_start: 0.7645 (tmm) cc_final: 0.7114 (tpp) outliers start: 28 outliers final: 17 residues processed: 155 average time/residue: 0.9007 time to fit residues: 152.1019 Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 299 VAL Chi-restraints excluded: chain A residue 303 ASP 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 638 LEU Chi-restraints excluded: chain A residue 658 GLU 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 C residue 15 SER 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: 0.7980 chunk 76 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.137305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118707 restraints weight = 13762.936| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.07 r_work: 0.3511 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8805 Z= 0.189 Angle : 0.555 8.006 11956 Z= 0.292 Chirality : 0.042 0.159 1354 Planarity : 0.003 0.048 1522 Dihedral : 4.204 22.492 1176 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.12 % Allowed : 19.26 % 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: 0.07 (0.26), residues: 1065 helix: 1.05 (0.24), residues: 509 sheet: -0.52 (0.51), residues: 97 loop : -0.93 (0.28), residues: 459 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 0.016 0.001 PHE A 741 TYR 0.026 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 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8085 (tp) cc_final: 0.7797 (tp) REVERT: A 541 GLN cc_start: 0.6784 (tt0) cc_final: 0.6507 (tt0) REVERT: A 705 ASN cc_start: 0.8319 (m110) cc_final: 0.8001 (m110) REVERT: A 818 MET cc_start: 0.6564 (ptt) cc_final: 0.6046 (pmt) REVERT: A 882 HIS cc_start: 0.7314 (m-70) cc_final: 0.7031 (m170) REVERT: C 3 MET cc_start: 0.6817 (tpp) cc_final: 0.6580 (tpp) REVERT: D 101 ASP cc_start: 0.8144 (p0) cc_final: 0.7830 (p0) REVERT: B 154 TRP cc_start: 0.7655 (OUTLIER) cc_final: 0.6688 (m100) REVERT: B 174 MET cc_start: 0.7639 (tmm) cc_final: 0.7177 (tpp) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.9599 time to fit residues: 143.8027 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 638 LEU Chi-restraints excluded: chain A residue 658 GLU 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 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: 0.7980 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.139435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121022 restraints weight = 13721.907| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.06 r_work: 0.3543 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8805 Z= 0.156 Angle : 0.552 9.505 11956 Z= 0.288 Chirality : 0.041 0.153 1354 Planarity : 0.003 0.050 1522 Dihedral : 4.013 19.057 1176 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.80 % Allowed : 19.89 % Favored : 78.31 % 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: 0.27 (0.26), residues: 1065 helix: 1.23 (0.23), residues: 509 sheet: -0.52 (0.51), residues: 97 loop : -0.82 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.011 0.001 TYR A 788 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 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 705 ASN cc_start: 0.8326 (m110) cc_final: 0.7999 (m110) REVERT: A 818 MET cc_start: 0.6548 (ptt) cc_final: 0.6026 (pmt) REVERT: A 882 HIS cc_start: 0.7325 (m-70) cc_final: 0.7042 (m170) REVERT: D 101 ASP cc_start: 0.8131 (p0) cc_final: 0.7822 (p0) REVERT: B 87 MET cc_start: 0.8262 (mtp) cc_final: 0.8049 (mtp) REVERT: B 154 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.6086 (m100) REVERT: B 174 MET cc_start: 0.7689 (tmm) cc_final: 0.7290 (tpp) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.9011 time to fit residues: 137.4481 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 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 613 HIS Chi-restraints excluded: chain A residue 658 GLU 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 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: 6.9990 chunk 58 optimal weight: 0.0030 chunk 31 optimal weight: 0.2980 chunk 26 optimal weight: 0.0980 chunk 89 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.140328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121936 restraints weight = 13818.794| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.07 r_work: 0.3560 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8805 Z= 0.146 Angle : 0.552 8.628 11956 Z= 0.285 Chirality : 0.041 0.141 1354 Planarity : 0.003 0.051 1522 Dihedral : 3.920 18.599 1176 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.48 % Allowed : 20.63 % Favored : 77.88 % 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: 0.44 (0.26), residues: 1065 helix: 1.36 (0.23), residues: 508 sheet: -0.55 (0.50), residues: 97 loop : -0.69 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.009 0.001 HIS A 613 PHE 0.014 0.001 PHE A 741 TYR 0.010 0.001 TYR A 515 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: 5974.99 seconds wall clock time: 102 minutes 48.62 seconds (6168.62 seconds total)