Starting phenix.real_space_refine on Wed Feb 4 01:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ndz_49290/02_2026/9ndz_49290_neut.cif" } resolution = 3.0 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= 0.020 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 30 5.16 5 C 5176 2.51 5 N 1445 2.21 5 O 1399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8050 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2754 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 328} Chain breaks: 6 Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5296 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 644} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 8050 At special positions: 0 Unit cell: (93.312, 103.518, 131.949, 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 30 16.00 O 1399 8.00 N 1445 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 250.1 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 43.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.740A pdb=" N LYS A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.673A pdb=" N LYS A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.508A pdb=" N ALA A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.674A pdb=" N ILE A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.642A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 793 removed outlier: 3.503A pdb=" N MET A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 860 through 861 No H-bonds generated for 'chain 'A' and resid 860 through 861' Processing helix chain 'A' and resid 862 through 867 removed outlier: 4.004A pdb=" N HIS A 867 " --> pdb=" O ARG A 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.634A pdb=" N TRP C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.704A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 267 through 283 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.585A pdb=" N VAL C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.741A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 412 through 426 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 435 through 448 Processing helix chain 'C' and resid 451 through 469 removed outlier: 3.629A pdb=" N GLY C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 469 through 492 removed outlier: 3.585A pdb=" N ARG C 473 " --> pdb=" O CYS C 469 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 588 through 607 Processing helix chain 'C' and resid 618 through 638 Processing helix chain 'C' and resid 642 through 647 removed outlier: 3.585A pdb=" N TRP C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 673 removed outlier: 3.515A pdb=" N ARG C 665 " --> pdb=" O THR C 662 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY C 667 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 668 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 671 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 732 Processing helix chain 'C' and resid 746 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 425 removed outlier: 6.617A pdb=" N ARG A 421 " --> pdb=" O HIS A 885 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 773 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER A 886 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 456 removed outlier: 6.614A pdb=" N CYS A 451 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 535 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 627 Processing sheet with id=AA4, first strand: chain 'A' and resid 624 through 627 removed outlier: 5.371A pdb=" N GLY A 761 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 675 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 56 removed outlier: 7.845A pdb=" N TYR C 30 " --> pdb=" O TRP C 22 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TRP C 22 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS C 32 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA C 20 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU C 34 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 18 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR C 36 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 16 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 38 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 210 removed outlier: 3.532A pdb=" N VAL C 199 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 196 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 259 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 230 through 237 Processing sheet with id=AA8, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.595A pdb=" N THR C 578 " --> pdb=" O ASN C 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 497 through 501 removed outlier: 6.585A pdb=" N TRP C 507 " --> pdb=" O CYS C 499 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY C 501 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 405 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL C 557 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 407 " --> pdb=" O GLU C 555 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 648 through 650 391 hydrogen bonds defined for protein. 1074 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: 1.09 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1293 1.28 - 1.41: 2141 1.41 - 1.54: 4778 1.54 - 1.68: 7 1.68 - 1.81: 39 Bond restraints: 8258 Sorted by residual: bond pdb=" C TRP C 384 " pdb=" N HIS C 385 " ideal model delta sigma weight residual 1.329 1.148 0.180 1.35e-02 5.49e+03 1.79e+02 bond pdb=" CA PHE C 226 " pdb=" C PHE C 226 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.46e+01 bond pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.08e-02 8.57e+03 1.44e+01 bond pdb=" CA PHE C 208 " pdb=" CB PHE C 208 " ideal model delta sigma weight residual 1.527 1.447 0.080 2.48e-02 1.63e+03 1.04e+01 bond pdb=" C ASN A 807 " pdb=" N PHE A 808 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.79e-02 3.12e+03 1.04e+01 ... (remaining 8253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 10979 2.93 - 5.86: 266 5.86 - 8.80: 30 8.80 - 11.73: 8 11.73 - 14.66: 1 Bond angle restraints: 11284 Sorted by residual: angle pdb=" N VAL A 815 " pdb=" CA VAL A 815 " pdb=" C VAL A 815 " ideal model delta sigma weight residual 113.20 106.03 7.17 9.60e-01 1.09e+00 5.57e+01 angle pdb=" C ALA A 670 " pdb=" N TYR A 671 " pdb=" CA TYR A 671 " ideal model delta sigma weight residual 120.94 111.43 9.51 1.90e+00 2.77e-01 2.51e+01 angle pdb=" C GLN A 512 " pdb=" N GLN A 513 " pdb=" CA GLN A 513 " ideal model delta sigma weight residual 121.54 112.15 9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" N PRO A 473 " pdb=" CA PRO A 473 " pdb=" C PRO A 473 " ideal model delta sigma weight residual 113.98 120.20 -6.22 1.29e+00 6.01e-01 2.32e+01 angle pdb=" C ALA C 86 " pdb=" N SER C 87 " pdb=" CA SER C 87 " ideal model delta sigma weight residual 123.30 129.38 -6.08 1.44e+00 4.82e-01 1.78e+01 ... (remaining 11279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4444 15.12 - 30.24: 346 30.24 - 45.36: 76 45.36 - 60.48: 15 60.48 - 75.60: 5 Dihedral angle restraints: 4886 sinusoidal: 1856 harmonic: 3030 Sorted by residual: dihedral pdb=" CA SER C 87 " pdb=" C SER C 87 " pdb=" N PRO C 88 " pdb=" CA PRO C 88 " ideal model delta harmonic sigma weight residual -180.00 -146.71 -33.29 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA GLN A 512 " pdb=" C GLN A 512 " pdb=" N GLN A 513 " pdb=" CA GLN A 513 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ARG C 79 " pdb=" C ARG C 79 " pdb=" N ALA C 80 " pdb=" CA ALA C 80 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 4883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 873 0.067 - 0.134: 343 0.134 - 0.202: 58 0.202 - 0.269: 5 0.269 - 0.336: 2 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CB ILE A 760 " pdb=" CA ILE A 760 " pdb=" CG1 ILE A 760 " pdb=" CG2 ILE A 760 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CG LEU C 89 " pdb=" CB LEU C 89 " pdb=" CD1 LEU C 89 " pdb=" CD2 LEU C 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA PRO A 473 " pdb=" N PRO A 473 " pdb=" C PRO A 473 " pdb=" CB PRO A 473 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1278 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 83 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 84 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 86 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ALA C 86 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA C 86 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 555 " 0.032 2.00e-02 2.50e+03 1.66e-02 6.89e+00 pdb=" CG TRP A 555 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 555 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 555 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 555 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 555 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 555 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 555 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 555 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 555 " 0.006 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 88 2.61 - 3.18: 7049 3.18 - 3.75: 12239 3.75 - 4.33: 17338 4.33 - 4.90: 28843 Nonbonded interactions: 65557 Sorted by model distance: nonbonded pdb=" OD1 ASP C 630 " pdb=" OH TYR C 739 " model vdw 2.036 3.040 nonbonded pdb=" OG SER C 66 " pdb=" OE1 GLN C 72 " model vdw 2.146 3.040 nonbonded pdb=" OD1 ASP C 657 " pdb=" NH2 ARG C 681 " model vdw 2.155 3.120 nonbonded pdb=" O VAL C 355 " pdb=" NH1 ARG C 440 " model vdw 2.189 3.120 nonbonded pdb=" O LEU C 109 " pdb=" OG1 THR C 113 " model vdw 2.199 3.040 ... (remaining 65552 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: 5.050 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.030 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 : 0.015 0.182 8258 Z= 0.662 Angle : 1.095 14.661 11284 Z= 0.565 Chirality : 0.069 0.336 1281 Planarity : 0.010 0.080 1467 Dihedral : 12.264 75.595 2926 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.55 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.75 (0.25), residues: 1026 helix: -1.54 (0.24), residues: 412 sheet: -1.07 (0.41), residues: 177 loop : -2.33 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 99 TYR 0.042 0.005 TYR C 558 PHE 0.029 0.004 PHE C 37 TRP 0.037 0.005 TRP A 555 HIS 0.015 0.004 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.01529 ( 8258) covalent geometry : angle 1.09538 (11284) hydrogen bonds : bond 0.17471 ( 387) hydrogen bonds : angle 8.26250 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.6923 (m-30) cc_final: 0.6494 (m-30) REVERT: A 554 ASP cc_start: 0.7070 (t0) cc_final: 0.6818 (t0) REVERT: A 630 ASP cc_start: 0.7008 (t0) cc_final: 0.6626 (t0) REVERT: C 132 LEU cc_start: 0.7956 (mp) cc_final: 0.7693 (mt) REVERT: C 654 GLU cc_start: 0.5751 (mp0) cc_final: 0.5511 (mp0) REVERT: C 719 ILE cc_start: 0.8084 (mt) cc_final: 0.7876 (mt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.5167 time to fit residues: 139.2092 Evaluate side-chains 207 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 545 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108772 restraints weight = 12156.733| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.80 r_work: 0.3333 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8258 Z= 0.198 Angle : 0.717 7.140 11284 Z= 0.368 Chirality : 0.047 0.175 1281 Planarity : 0.008 0.066 1467 Dihedral : 5.689 31.592 1159 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.07 % Favored : 94.74 % Rotamer: Outliers : 3.36 % Allowed : 10.45 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.91 (0.26), residues: 1026 helix: -0.55 (0.25), residues: 419 sheet: -0.92 (0.40), residues: 170 loop : -2.05 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.013 0.002 TYR A 609 PHE 0.016 0.002 PHE A 866 TRP 0.017 0.002 TRP C 98 HIS 0.005 0.001 HIS C 560 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8258) covalent geometry : angle 0.71651 (11284) hydrogen bonds : bond 0.05027 ( 387) hydrogen bonds : angle 5.72262 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.205 Fit side-chains REVERT: A 455 ASP cc_start: 0.8177 (m-30) cc_final: 0.7912 (m-30) REVERT: A 540 MET cc_start: 0.8110 (mmm) cc_final: 0.7857 (mmt) REVERT: A 554 ASP cc_start: 0.7463 (t0) cc_final: 0.7211 (t0) REVERT: A 781 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7054 (mtp85) REVERT: A 804 TYR cc_start: 0.8324 (m-80) cc_final: 0.8013 (m-80) REVERT: A 841 LEU cc_start: 0.8464 (mt) cc_final: 0.8260 (mm) REVERT: C 9 VAL cc_start: 0.8182 (m) cc_final: 0.7899 (p) REVERT: C 161 ASP cc_start: 0.7832 (t0) cc_final: 0.7576 (t70) REVERT: C 303 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7852 (mtt-85) REVERT: C 313 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7948 (pp) REVERT: C 384 TRP cc_start: 0.8170 (t60) cc_final: 0.7818 (t60) REVERT: C 473 ARG cc_start: 0.6904 (tpp80) cc_final: 0.6512 (ttm170) REVERT: C 569 VAL cc_start: 0.8473 (t) cc_final: 0.8223 (p) REVERT: C 715 ILE cc_start: 0.8374 (mp) cc_final: 0.8155 (mp) REVERT: C 719 ILE cc_start: 0.8255 (mt) cc_final: 0.8034 (mt) outliers start: 27 outliers final: 10 residues processed: 228 average time/residue: 0.4970 time to fit residues: 120.3260 Evaluate side-chains 220 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 0.0370 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.0030 overall best weight: 0.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109206 restraints weight = 12031.240| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.72 r_work: 0.3352 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8258 Z= 0.191 Angle : 0.661 6.539 11284 Z= 0.338 Chirality : 0.046 0.164 1281 Planarity : 0.007 0.062 1467 Dihedral : 5.253 28.507 1159 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 4.60 % Allowed : 14.30 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.49 (0.26), residues: 1026 helix: -0.01 (0.26), residues: 419 sheet: -0.93 (0.38), residues: 179 loop : -1.97 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 529 TYR 0.016 0.002 TYR C 256 PHE 0.016 0.002 PHE A 866 TRP 0.012 0.002 TRP C 98 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8258) covalent geometry : angle 0.66140 (11284) hydrogen bonds : bond 0.04400 ( 387) hydrogen bonds : angle 5.20316 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: A 550 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8282 (pp) REVERT: A 554 ASP cc_start: 0.7481 (t0) cc_final: 0.7170 (t0) REVERT: A 781 ARG cc_start: 0.7429 (mtp85) cc_final: 0.7104 (mtp85) REVERT: A 804 TYR cc_start: 0.8329 (m-80) cc_final: 0.7973 (m-80) REVERT: C 384 TRP cc_start: 0.8160 (t60) cc_final: 0.7863 (t60) REVERT: C 424 LEU cc_start: 0.8527 (mt) cc_final: 0.8300 (mm) REVERT: C 715 ILE cc_start: 0.8361 (mp) cc_final: 0.8128 (mp) outliers start: 37 outliers final: 15 residues processed: 227 average time/residue: 0.5521 time to fit residues: 132.8356 Evaluate side-chains 233 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS C 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109058 restraints weight = 12303.374| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.75 r_work: 0.3348 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8258 Z= 0.186 Angle : 0.648 8.308 11284 Z= 0.328 Chirality : 0.046 0.162 1281 Planarity : 0.007 0.059 1467 Dihedral : 5.049 27.692 1159 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 5.47 % Allowed : 16.04 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.25 (0.27), residues: 1026 helix: 0.20 (0.26), residues: 422 sheet: -0.87 (0.38), residues: 179 loop : -1.82 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 640 TYR 0.013 0.002 TYR C 256 PHE 0.015 0.001 PHE A 868 TRP 0.013 0.002 TRP C 98 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8258) covalent geometry : angle 0.64846 (11284) hydrogen bonds : bond 0.04221 ( 387) hydrogen bonds : angle 5.00936 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: A 540 MET cc_start: 0.8257 (mmm) cc_final: 0.8026 (mmt) REVERT: A 554 ASP cc_start: 0.7466 (t0) cc_final: 0.7183 (t0) REVERT: A 781 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7172 (mtp85) REVERT: A 804 TYR cc_start: 0.8326 (m-80) cc_final: 0.7953 (m-80) REVERT: C 9 VAL cc_start: 0.8194 (m) cc_final: 0.7911 (p) REVERT: C 384 TRP cc_start: 0.8172 (t60) cc_final: 0.7811 (t60) REVERT: C 424 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8288 (mm) REVERT: C 464 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (t0) outliers start: 44 outliers final: 22 residues processed: 225 average time/residue: 0.5313 time to fit residues: 126.7489 Evaluate side-chains 219 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 658 GLN C 242 HIS ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109520 restraints weight = 12115.270| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.72 r_work: 0.3353 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8258 Z= 0.197 Angle : 0.653 7.510 11284 Z= 0.331 Chirality : 0.047 0.280 1281 Planarity : 0.007 0.061 1467 Dihedral : 4.979 27.286 1159 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.54 % Rotamer: Outliers : 4.48 % Allowed : 18.16 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.11 (0.27), residues: 1026 helix: 0.31 (0.26), residues: 422 sheet: -0.82 (0.37), residues: 187 loop : -1.74 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 585 TYR 0.014 0.002 TYR C 256 PHE 0.015 0.002 PHE A 868 TRP 0.012 0.002 TRP C 98 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8258) covalent geometry : angle 0.65350 (11284) hydrogen bonds : bond 0.04199 ( 387) hydrogen bonds : angle 4.93570 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 540 MET cc_start: 0.8271 (mmm) cc_final: 0.8022 (mmt) REVERT: A 554 ASP cc_start: 0.7445 (t0) cc_final: 0.7168 (t0) REVERT: A 620 LEU cc_start: 0.7971 (mt) cc_final: 0.7731 (mt) REVERT: A 630 ASP cc_start: 0.7726 (t0) cc_final: 0.7379 (t0) REVERT: C 9 VAL cc_start: 0.8202 (m) cc_final: 0.7921 (p) REVERT: C 110 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7603 (pt0) REVERT: C 187 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: C 188 THR cc_start: 0.8180 (t) cc_final: 0.7908 (p) REVERT: C 378 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7290 (mtp-110) REVERT: C 384 TRP cc_start: 0.8186 (t60) cc_final: 0.7822 (t60) REVERT: C 424 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8301 (mm) REVERT: C 464 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7961 (t0) outliers start: 36 outliers final: 20 residues processed: 213 average time/residue: 0.5291 time to fit residues: 119.7433 Evaluate side-chains 225 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 658 GLN C 242 HIS ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110242 restraints weight = 12004.337| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.70 r_work: 0.3365 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8258 Z= 0.158 Angle : 0.621 7.030 11284 Z= 0.313 Chirality : 0.045 0.237 1281 Planarity : 0.006 0.061 1467 Dihedral : 4.806 26.181 1159 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.22 % Rotamer: Outliers : 5.10 % Allowed : 18.66 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.95 (0.27), residues: 1026 helix: 0.45 (0.26), residues: 428 sheet: -0.77 (0.37), residues: 185 loop : -1.67 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 585 TYR 0.013 0.002 TYR A 804 PHE 0.014 0.001 PHE A 868 TRP 0.012 0.001 TRP C 98 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8258) covalent geometry : angle 0.62141 (11284) hydrogen bonds : bond 0.03965 ( 387) hydrogen bonds : angle 4.79785 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: A 540 MET cc_start: 0.8263 (mmm) cc_final: 0.8005 (mmt) REVERT: A 554 ASP cc_start: 0.7416 (t0) cc_final: 0.7156 (t0) REVERT: A 620 LEU cc_start: 0.7945 (mt) cc_final: 0.7700 (mt) REVERT: A 630 ASP cc_start: 0.7645 (t0) cc_final: 0.7338 (t70) REVERT: C 9 VAL cc_start: 0.8208 (m) cc_final: 0.7919 (p) REVERT: C 13 VAL cc_start: 0.7640 (t) cc_final: 0.7371 (t) REVERT: C 89 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7522 (mt) REVERT: C 110 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7597 (pt0) REVERT: C 187 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: C 384 TRP cc_start: 0.8188 (t60) cc_final: 0.7830 (t60) REVERT: C 424 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (mm) outliers start: 41 outliers final: 24 residues processed: 220 average time/residue: 0.5270 time to fit residues: 123.3713 Evaluate side-chains 231 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 86 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110158 restraints weight = 12197.365| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.75 r_work: 0.3362 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8258 Z= 0.157 Angle : 0.632 9.096 11284 Z= 0.315 Chirality : 0.046 0.310 1281 Planarity : 0.006 0.060 1467 Dihedral : 4.734 25.204 1159 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.68 % Favored : 95.13 % Rotamer: Outliers : 4.85 % Allowed : 19.15 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.83 (0.27), residues: 1026 helix: 0.58 (0.27), residues: 422 sheet: -0.78 (0.37), residues: 185 loop : -1.57 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 640 TYR 0.014 0.002 TYR A 804 PHE 0.014 0.001 PHE A 868 TRP 0.011 0.001 TRP C 98 HIS 0.004 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8258) covalent geometry : angle 0.63170 (11284) hydrogen bonds : bond 0.03891 ( 387) hydrogen bonds : angle 4.74657 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: A 540 MET cc_start: 0.8258 (mmm) cc_final: 0.7998 (mmt) REVERT: A 554 ASP cc_start: 0.7437 (t0) cc_final: 0.7198 (t0) REVERT: A 620 LEU cc_start: 0.7989 (mt) cc_final: 0.7778 (mt) REVERT: A 630 ASP cc_start: 0.7675 (t0) cc_final: 0.7368 (t70) REVERT: C 9 VAL cc_start: 0.8209 (m) cc_final: 0.7913 (p) REVERT: C 13 VAL cc_start: 0.7644 (t) cc_final: 0.7393 (t) REVERT: C 89 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7521 (mt) REVERT: C 187 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: C 188 THR cc_start: 0.8184 (t) cc_final: 0.7895 (p) REVERT: C 256 TYR cc_start: 0.8000 (p90) cc_final: 0.7745 (p90) REVERT: C 384 TRP cc_start: 0.8177 (t60) cc_final: 0.7823 (t60) REVERT: C 424 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (mm) outliers start: 39 outliers final: 23 residues processed: 226 average time/residue: 0.5523 time to fit residues: 132.3937 Evaluate side-chains 222 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS A 417 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN C 242 HIS ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110052 restraints weight = 12131.038| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.75 r_work: 0.3365 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8258 Z= 0.158 Angle : 0.635 9.160 11284 Z= 0.317 Chirality : 0.046 0.296 1281 Planarity : 0.006 0.060 1467 Dihedral : 4.686 24.660 1159 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.32 % Rotamer: Outliers : 4.10 % Allowed : 20.40 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.76 (0.27), residues: 1026 helix: 0.70 (0.27), residues: 414 sheet: -0.78 (0.37), residues: 185 loop : -1.54 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 677 TYR 0.016 0.002 TYR C 739 PHE 0.014 0.001 PHE A 868 TRP 0.011 0.001 TRP C 98 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8258) covalent geometry : angle 0.63489 (11284) hydrogen bonds : bond 0.03867 ( 387) hydrogen bonds : angle 4.72257 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: A 540 MET cc_start: 0.8246 (mmm) cc_final: 0.7998 (mmt) REVERT: A 554 ASP cc_start: 0.7449 (t0) cc_final: 0.7214 (t0) REVERT: A 620 LEU cc_start: 0.8005 (mt) cc_final: 0.7777 (mt) REVERT: A 630 ASP cc_start: 0.7642 (t0) cc_final: 0.7330 (t70) REVERT: C 13 VAL cc_start: 0.7670 (t) cc_final: 0.7429 (t) REVERT: C 89 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7514 (mt) REVERT: C 187 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: C 256 TYR cc_start: 0.8004 (p90) cc_final: 0.7730 (p90) REVERT: C 384 TRP cc_start: 0.8189 (t60) cc_final: 0.7817 (t60) REVERT: C 424 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (mm) outliers start: 33 outliers final: 24 residues processed: 211 average time/residue: 0.4587 time to fit residues: 102.9272 Evaluate side-chains 225 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 57 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109836 restraints weight = 12231.035| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.74 r_work: 0.3361 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8258 Z= 0.170 Angle : 0.650 9.555 11284 Z= 0.325 Chirality : 0.046 0.339 1281 Planarity : 0.006 0.061 1467 Dihedral : 4.695 24.540 1159 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 4.48 % Allowed : 20.65 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.74 (0.27), residues: 1026 helix: 0.68 (0.27), residues: 414 sheet: -0.74 (0.37), residues: 187 loop : -1.52 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 677 TYR 0.017 0.002 TYR C 739 PHE 0.017 0.001 PHE C 664 TRP 0.011 0.001 TRP C 98 HIS 0.006 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8258) covalent geometry : angle 0.64961 (11284) hydrogen bonds : bond 0.03928 ( 387) hydrogen bonds : angle 4.76009 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: A 540 MET cc_start: 0.8238 (mmm) cc_final: 0.8015 (mmt) REVERT: A 554 ASP cc_start: 0.7434 (t0) cc_final: 0.7191 (t0) REVERT: A 620 LEU cc_start: 0.7976 (mt) cc_final: 0.7753 (mt) REVERT: A 630 ASP cc_start: 0.7661 (t0) cc_final: 0.7356 (t70) REVERT: C 9 VAL cc_start: 0.8199 (m) cc_final: 0.7906 (p) REVERT: C 13 VAL cc_start: 0.7680 (t) cc_final: 0.7435 (t) REVERT: C 89 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7528 (mt) REVERT: C 187 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: C 188 THR cc_start: 0.8223 (t) cc_final: 0.7932 (p) REVERT: C 384 TRP cc_start: 0.8165 (t60) cc_final: 0.7826 (t60) REVERT: C 424 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8298 (mm) outliers start: 36 outliers final: 23 residues processed: 218 average time/residue: 0.4631 time to fit residues: 107.3514 Evaluate side-chains 229 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.1980 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109679 restraints weight = 12266.818| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.80 r_work: 0.3350 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8258 Z= 0.154 Angle : 0.644 11.257 11284 Z= 0.321 Chirality : 0.046 0.328 1281 Planarity : 0.006 0.060 1467 Dihedral : 4.635 24.222 1159 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.71 % Rotamer: Outliers : 3.73 % Allowed : 21.89 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.65 (0.27), residues: 1026 helix: 0.75 (0.27), residues: 414 sheet: -0.82 (0.36), residues: 197 loop : -1.39 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 529 TYR 0.018 0.002 TYR C 739 PHE 0.015 0.001 PHE C 664 TRP 0.011 0.001 TRP C 98 HIS 0.004 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8258) covalent geometry : angle 0.64367 (11284) hydrogen bonds : bond 0.03828 ( 387) hydrogen bonds : angle 4.71374 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: A 540 MET cc_start: 0.8203 (mmm) cc_final: 0.7959 (mmt) REVERT: A 620 LEU cc_start: 0.8057 (mt) cc_final: 0.7832 (mt) REVERT: A 630 ASP cc_start: 0.7626 (t0) cc_final: 0.7307 (t70) REVERT: C 9 VAL cc_start: 0.8179 (m) cc_final: 0.7884 (p) REVERT: C 13 VAL cc_start: 0.7655 (t) cc_final: 0.7400 (t) REVERT: C 89 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7496 (mt) REVERT: C 188 THR cc_start: 0.8201 (t) cc_final: 0.7893 (p) REVERT: C 384 TRP cc_start: 0.8164 (t60) cc_final: 0.7818 (t60) REVERT: C 424 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8247 (mm) REVERT: C 600 ASP cc_start: 0.7558 (m-30) cc_final: 0.7340 (t70) outliers start: 30 outliers final: 22 residues processed: 209 average time/residue: 0.4431 time to fit residues: 98.4497 Evaluate side-chains 215 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 chunk 32 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.0532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113741 restraints weight = 12149.240| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.79 r_work: 0.3418 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8258 Z= 0.108 Angle : 0.611 12.362 11284 Z= 0.299 Chirality : 0.044 0.322 1281 Planarity : 0.006 0.058 1467 Dihedral : 4.286 24.079 1159 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.61 % Favored : 96.20 % Rotamer: Outliers : 2.24 % Allowed : 23.63 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -0.36 (0.28), residues: 1026 helix: 1.00 (0.27), residues: 418 sheet: -0.72 (0.36), residues: 197 loop : -1.22 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 529 TYR 0.013 0.001 TYR A 804 PHE 0.014 0.001 PHE A 866 TRP 0.009 0.001 TRP C 453 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8258) covalent geometry : angle 0.61129 (11284) hydrogen bonds : bond 0.03237 ( 387) hydrogen bonds : angle 4.48138 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.93 seconds wall clock time: 53 minutes 14.53 seconds (3194.53 seconds total)