Starting phenix.real_space_refine on Tue Mar 3 20:33:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_30127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_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 { model { file = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_30127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_30127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_30127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m71_30127/03_2026/6m71_30127.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ARG:plan': 2, 'GLU:plan': 1, '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: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.81, per 1000 atoms: 0.21 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: 0.53 Conformation dependent library (CDL) restraints added in 301.0 milliseconds 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: 0.32 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: 1.04 Time building geometry restraints manager: 0.76 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: 1.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- 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 : 0.011 0.731 8807 Z= 0.556 Angle : 0.630 14.185 11960 Z= 0.370 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 116 TYR 0.018 0.001 TYR A 788 PHE 0.016 0.001 PHE A 652 TRP 0.014 0.001 TRP B 154 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8805) covalent geometry : angle 0.59198 (11956) SS BOND : bond 0.70578 ( 2) SS BOND : angle 11.77885 ( 4) hydrogen bonds : bond 0.14970 ( 393) hydrogen bonds : angle 6.27878 ( 1104) *********************** 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 : 0.275 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: 0.5150 time to fit residues: 93.5888 Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.134657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115913 restraints weight = 13886.850| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.07 r_work: 0.3468 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8807 Z= 0.175 Angle : 0.567 7.552 11960 Z= 0.305 Chirality : 0.044 0.198 1354 Planarity : 0.004 0.039 1522 Dihedral : 4.669 25.121 1176 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 12.91 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1065 helix: 0.06 (0.23), residues: 498 sheet: -1.50 (0.45), residues: 82 loop : -2.06 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.018 0.002 TYR A 770 PHE 0.017 0.002 PHE A 741 TRP 0.017 0.001 TRP B 154 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8805) covalent geometry : angle 0.56640 (11956) SS BOND : bond 0.01278 ( 2) SS BOND : angle 0.97535 ( 4) hydrogen bonds : bond 0.04137 ( 393) hydrogen bonds : angle 4.75629 ( 1104) *********************** 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 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 333 ILE cc_start: 0.8200 (pt) cc_final: 0.7961 (pt) REVERT: A 372 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 882 HIS cc_start: 0.7349 (m-70) cc_final: 0.7008 (m170) REVERT: C 3 MET cc_start: 0.6797 (tpp) cc_final: 0.6526 (tpp) REVERT: C 47 GLU cc_start: 0.7021 (mp0) cc_final: 0.6807 (mp0) REVERT: C 52 MET cc_start: 0.8399 (tpp) cc_final: 0.7278 (tmm) REVERT: D 101 ASP cc_start: 0.8200 (p0) cc_final: 0.7802 (p0) outliers start: 23 outliers final: 10 residues processed: 152 average time/residue: 0.4646 time to fit residues: 76.2705 Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.137217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118540 restraints weight = 13623.985| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.06 r_work: 0.3509 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8807 Z= 0.121 Angle : 0.515 7.176 11960 Z= 0.274 Chirality : 0.042 0.186 1354 Planarity : 0.003 0.039 1522 Dihedral : 4.348 21.429 1176 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 14.18 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1065 helix: 0.69 (0.24), residues: 499 sheet: -1.44 (0.47), residues: 91 loop : -1.56 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 555 TYR 0.016 0.001 TYR A 420 PHE 0.015 0.001 PHE A 368 TRP 0.013 0.001 TRP B 154 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8805) covalent geometry : angle 0.51491 (11956) SS BOND : bond 0.00428 ( 2) SS BOND : angle 0.93761 ( 4) hydrogen bonds : bond 0.03462 ( 393) hydrogen bonds : angle 4.43505 ( 1104) *********************** 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: 27 poor density : 141 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 372 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 882 HIS cc_start: 0.7312 (m-70) cc_final: 0.7017 (m170) REVERT: C 3 MET cc_start: 0.6599 (tpp) cc_final: 0.6289 (tpp) REVERT: C 47 GLU cc_start: 0.6960 (mp0) cc_final: 0.6742 (mp0) REVERT: D 101 ASP cc_start: 0.8146 (p0) cc_final: 0.7881 (p0) REVERT: B 82 LYS cc_start: 0.8032 (tptp) cc_final: 0.7795 (tppt) REVERT: B 96 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6754 (mtp180) REVERT: B 154 TRP cc_start: 0.7747 (OUTLIER) cc_final: 0.6716 (m100) outliers start: 27 outliers final: 11 residues processed: 160 average time/residue: 0.4554 time to fit residues: 78.8007 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 154 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- 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 ** 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 = 0.3793 r_free = 0.3793 target = 0.134519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115524 restraints weight = 14025.850| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.12 r_work: 0.3449 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8807 Z= 0.189 Angle : 0.559 7.067 11960 Z= 0.300 Chirality : 0.044 0.155 1354 Planarity : 0.004 0.041 1522 Dihedral : 4.536 25.286 1176 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 15.13 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1065 helix: 0.67 (0.24), residues: 499 sheet: -1.39 (0.49), residues: 91 loop : -1.44 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.021 0.002 TYR A 420 PHE 0.018 0.002 PHE A 741 TRP 0.016 0.001 TRP B 154 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8805) covalent geometry : angle 0.55863 (11956) SS BOND : bond 0.00642 ( 2) SS BOND : angle 1.30379 ( 4) hydrogen bonds : bond 0.04051 ( 393) hydrogen bonds : angle 4.56298 ( 1104) *********************** 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 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 882 HIS cc_start: 0.7393 (m-70) cc_final: 0.7061 (m170) REVERT: C 3 MET cc_start: 0.6945 (tpp) cc_final: 0.6692 (tpp) REVERT: C 47 GLU cc_start: 0.6998 (mp0) cc_final: 0.6760 (mp0) REVERT: D 101 ASP cc_start: 0.8101 (p0) cc_final: 0.7777 (p0) REVERT: B 82 LYS cc_start: 0.8055 (tptp) cc_final: 0.7827 (tppt) REVERT: B 96 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6782 (mtp180) REVERT: B 154 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.7721 (m100) outliers start: 32 outliers final: 16 residues processed: 155 average time/residue: 0.4512 time to fit residues: 75.5604 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 468 GLN A 613 HIS A 705 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117004 restraints weight = 13812.702| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.08 r_work: 0.3473 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8807 Z= 0.141 Angle : 0.527 7.217 11960 Z= 0.281 Chirality : 0.042 0.157 1354 Planarity : 0.003 0.040 1522 Dihedral : 4.376 23.005 1176 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 17.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1065 helix: 0.83 (0.24), residues: 501 sheet: -1.26 (0.50), residues: 91 loop : -1.24 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.024 0.001 TYR A 420 PHE 0.016 0.002 PHE A 741 TRP 0.014 0.001 TRP B 154 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8805) covalent geometry : angle 0.52712 (11956) SS BOND : bond 0.00515 ( 2) SS BOND : angle 1.18506 ( 4) hydrogen bonds : bond 0.03619 ( 393) hydrogen bonds : angle 4.43785 ( 1104) *********************** 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: 32 poor density : 137 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8090 (tp) cc_final: 0.7800 (tp) REVERT: A 372 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 818 MET cc_start: 0.6762 (ptt) cc_final: 0.6213 (pmt) REVERT: A 882 HIS cc_start: 0.7356 (m-70) cc_final: 0.7009 (m170) REVERT: C 3 MET cc_start: 0.6852 (tpp) cc_final: 0.6526 (tpp) REVERT: C 47 GLU cc_start: 0.7043 (mp0) cc_final: 0.6729 (mp0) REVERT: D 101 ASP cc_start: 0.8125 (p0) cc_final: 0.7830 (p0) REVERT: B 96 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6753 (mtp180) REVERT: B 154 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.7452 (m100) outliers start: 32 outliers final: 19 residues processed: 157 average time/residue: 0.4421 time to fit residues: 74.9374 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 : 0.253 ------------------------------------------------------------------------------- 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 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 85 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114174 restraints weight = 13936.033| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.09 r_work: 0.3444 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8807 Z= 0.234 Angle : 0.609 7.356 11960 Z= 0.325 Chirality : 0.045 0.156 1354 Planarity : 0.004 0.041 1522 Dihedral : 4.660 27.735 1176 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.60 % Allowed : 17.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.25), residues: 1065 helix: 0.53 (0.23), residues: 508 sheet: -1.13 (0.51), residues: 82 loop : -1.42 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.025 0.002 TYR A 420 PHE 0.020 0.002 PHE A 741 TRP 0.018 0.002 TRP B 154 HIS 0.010 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 8805) covalent geometry : angle 0.60884 (11956) SS BOND : bond 0.00739 ( 2) SS BOND : angle 1.51631 ( 4) hydrogen bonds : bond 0.04370 ( 393) hydrogen bonds : angle 4.73472 ( 1104) *********************** 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: 34 poor density : 127 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8203 (tp) cc_final: 0.7931 (tp) REVERT: A 340 PHE cc_start: 0.7598 (m-80) cc_final: 0.7300 (m-80) REVERT: A 566 MET cc_start: 0.8430 (mtp) cc_final: 0.8213 (mtp) REVERT: A 818 MET cc_start: 0.6841 (ptt) cc_final: 0.6335 (pmt) REVERT: A 882 HIS cc_start: 0.7464 (m-70) cc_final: 0.7119 (m170) REVERT: C 47 GLU cc_start: 0.7170 (mp0) cc_final: 0.6823 (mp0) REVERT: D 101 ASP cc_start: 0.8100 (p0) cc_final: 0.7781 (p0) REVERT: B 96 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6833 (mtp180) REVERT: B 154 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.7773 (m100) outliers start: 34 outliers final: 19 residues processed: 150 average time/residue: 0.4240 time to fit residues: 69.1827 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 C residue 15 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120425 restraints weight = 13873.605| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.10 r_work: 0.3525 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8807 Z= 0.110 Angle : 0.527 8.287 11960 Z= 0.277 Chirality : 0.041 0.157 1354 Planarity : 0.003 0.037 1522 Dihedral : 4.206 19.923 1176 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.49 % Allowed : 17.78 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1065 helix: 0.98 (0.24), residues: 503 sheet: -0.52 (0.49), residues: 97 loop : -1.13 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.022 0.001 TYR A 420 PHE 0.015 0.001 PHE A 741 TRP 0.011 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8805) covalent geometry : angle 0.52630 (11956) SS BOND : bond 0.00667 ( 2) SS BOND : angle 0.97850 ( 4) hydrogen bonds : bond 0.03189 ( 393) hydrogen bonds : angle 4.29538 ( 1104) *********************** 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 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.356 Fit side-chains REVERT: A 241 LEU cc_start: 0.8042 (tp) cc_final: 0.7761 (tp) REVERT: A 340 PHE cc_start: 0.7453 (m-80) cc_final: 0.7117 (m-80) REVERT: A 818 MET cc_start: 0.6718 (ptt) cc_final: 0.6214 (pmt) REVERT: A 882 HIS cc_start: 0.7322 (m-70) cc_final: 0.6988 (m170) REVERT: C 47 GLU cc_start: 0.7032 (mp0) cc_final: 0.6771 (mp0) REVERT: D 101 ASP cc_start: 0.8127 (p0) cc_final: 0.7885 (p0) REVERT: B 96 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6819 (mtp180) REVERT: B 154 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.6388 (m100) REVERT: B 174 MET cc_start: 0.7682 (tmm) cc_final: 0.7158 (tpp) outliers start: 33 outliers final: 13 residues processed: 158 average time/residue: 0.4165 time to fit residues: 71.6049 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 402 THR 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 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 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 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117015 restraints weight = 13831.729| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.07 r_work: 0.3489 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: 0.7993 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8807 Z= 0.158 Angle : 0.585 8.093 11960 Z= 0.308 Chirality : 0.043 0.157 1354 Planarity : 0.004 0.051 1522 Dihedral : 4.342 23.841 1176 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.33 % Allowed : 19.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1065 helix: 0.75 (0.23), residues: 517 sheet: -0.65 (0.54), residues: 87 loop : -1.09 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.014 0.001 TYR A 788 PHE 0.018 0.002 PHE A 741 TRP 0.016 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8805) covalent geometry : angle 0.58443 (11956) SS BOND : bond 0.00612 ( 2) SS BOND : angle 1.13930 ( 4) hydrogen bonds : bond 0.03748 ( 393) hydrogen bonds : angle 4.45285 ( 1104) *********************** 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 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.337 Fit side-chains REVERT: A 241 LEU cc_start: 0.8107 (tp) cc_final: 0.7831 (tp) REVERT: A 340 PHE cc_start: 0.7502 (m-80) cc_final: 0.7173 (m-80) REVERT: A 372 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7688 (mp) REVERT: A 818 MET cc_start: 0.6788 (ptt) cc_final: 0.6277 (pmt) REVERT: A 882 HIS cc_start: 0.7324 (m-70) cc_final: 0.7036 (m170) REVERT: C 47 GLU cc_start: 0.7148 (mp0) cc_final: 0.6884 (mp0) REVERT: D 101 ASP cc_start: 0.8128 (p0) cc_final: 0.7830 (p0) REVERT: B 96 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6832 (mtp180) REVERT: B 154 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.7304 (m100) REVERT: B 174 MET cc_start: 0.7666 (tmm) cc_final: 0.7172 (tpp) outliers start: 22 outliers final: 14 residues processed: 146 average time/residue: 0.4471 time to fit residues: 70.7794 Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.135234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116676 restraints weight = 13816.092| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.06 r_work: 0.3483 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8807 Z= 0.163 Angle : 0.580 7.258 11960 Z= 0.307 Chirality : 0.043 0.162 1354 Planarity : 0.004 0.050 1522 Dihedral : 4.381 24.448 1176 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.22 % Allowed : 20.00 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1065 helix: 0.74 (0.23), residues: 517 sheet: -0.70 (0.54), residues: 87 loop : -1.04 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.027 0.001 TYR A 420 PHE 0.017 0.002 PHE A 741 TRP 0.016 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8805) covalent geometry : angle 0.57922 (11956) SS BOND : bond 0.00622 ( 2) SS BOND : angle 1.18818 ( 4) hydrogen bonds : bond 0.03753 ( 393) hydrogen bonds : angle 4.49692 ( 1104) *********************** 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 : 0.345 Fit side-chains REVERT: A 241 LEU cc_start: 0.8136 (tp) cc_final: 0.7850 (tp) REVERT: A 340 PHE cc_start: 0.7545 (m-80) cc_final: 0.7234 (m-80) REVERT: A 818 MET cc_start: 0.6774 (ptt) cc_final: 0.6323 (pmt) REVERT: A 882 HIS cc_start: 0.7349 (m-70) cc_final: 0.7060 (m170) REVERT: C 47 GLU cc_start: 0.7052 (mp0) cc_final: 0.6830 (mp0) REVERT: D 101 ASP cc_start: 0.8126 (p0) cc_final: 0.7803 (p0) REVERT: B 96 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: B 154 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.7323 (m100) REVERT: B 174 MET cc_start: 0.7661 (tmm) cc_final: 0.7132 (tpp) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.4267 time to fit residues: 66.9852 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.136955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118464 restraints weight = 13770.158| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.06 r_work: 0.3505 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8807 Z= 0.132 Angle : 0.584 8.828 11960 Z= 0.305 Chirality : 0.042 0.162 1354 Planarity : 0.004 0.055 1522 Dihedral : 4.254 22.226 1176 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.90 % Allowed : 20.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1065 helix: 0.86 (0.23), residues: 516 sheet: -0.60 (0.55), residues: 87 loop : -0.96 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 21 TYR 0.024 0.001 TYR A 420 PHE 0.016 0.001 PHE A 741 TRP 0.014 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8805) covalent geometry : angle 0.58380 (11956) SS BOND : bond 0.00514 ( 2) SS BOND : angle 1.02870 ( 4) hydrogen bonds : bond 0.03505 ( 393) hydrogen bonds : angle 4.41614 ( 1104) ********************** 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 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.328 Fit side-chains REVERT: A 241 LEU cc_start: 0.8070 (tp) cc_final: 0.7773 (tp) REVERT: A 340 PHE cc_start: 0.7480 (m-80) cc_final: 0.7186 (m-80) REVERT: A 818 MET cc_start: 0.6744 (ptt) cc_final: 0.6245 (pmt) REVERT: A 882 HIS cc_start: 0.7312 (m-70) cc_final: 0.7025 (m170) REVERT: C 15 SER cc_start: 0.8537 (t) cc_final: 0.8312 (m) REVERT: D 101 ASP cc_start: 0.8127 (p0) cc_final: 0.7805 (p0) REVERT: B 92 PHE cc_start: 0.7903 (m-10) cc_final: 0.7684 (m-10) REVERT: B 96 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: B 154 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.6711 (m100) REVERT: B 174 MET cc_start: 0.7674 (tmm) cc_final: 0.7181 (tpp) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.4156 time to fit residues: 61.4973 Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.137823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119389 restraints weight = 13758.095| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.05 r_work: 0.3521 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8807 Z= 0.123 Angle : 0.581 9.400 11960 Z= 0.303 Chirality : 0.042 0.162 1354 Planarity : 0.004 0.058 1522 Dihedral : 4.145 20.555 1176 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1065 helix: 1.00 (0.23), residues: 509 sheet: -0.61 (0.55), residues: 87 loop : -0.87 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 21 TYR 0.025 0.001 TYR A 420 PHE 0.016 0.001 PHE A 766 TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8805) covalent geometry : angle 0.58049 (11956) SS BOND : bond 0.00462 ( 2) SS BOND : angle 0.96988 ( 4) hydrogen bonds : bond 0.03339 ( 393) hydrogen bonds : angle 4.35156 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.70 seconds wall clock time: 48 minutes 23.86 seconds (2903.86 seconds total)