Starting phenix.real_space_refine on Thu Feb 5 05:10:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og9_70458/02_2026/9og9_70458.map" } resolution = 2.93 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= 0.009 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 4706 2.51 5 N 1224 2.21 5 O 1342 1.98 5 H 7363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 14684 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 902, 14663 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 34, 'TRANS': 867} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 902, 14663 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 34, 'TRANS': 867} Chain breaks: 4 bond proxies already assigned to first conformer: 14787 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 414 " occ=0.50 ... (36 atoms not shown) pdb=" HZ BPHE A 414 " occ=0.50 Time building chain proxies: 4.04, per 1000 atoms: 0.28 Number of scatterers: 14684 At special positions: 0 Unit cell: (75.276, 109.224, 109.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 1342 8.00 N 1224 7.00 C 4706 6.00 H 7363 1.00 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: 1.29 Conformation dependent library (CDL) restraints added in 576.7 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 1 sheets defined 86.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.821A pdb=" N ASN A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.501A pdb=" N PHE A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.839A pdb=" N ILE A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.556A pdb=" N LEU A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.547A pdb=" N MET A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 312 through 340 removed outlier: 6.828A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 337 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.750A pdb=" N GLU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.575A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Proline residue: A 411 - end of helix removed outlier: 3.922A pdb=" N APHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 removed outlier: 3.814A pdb=" N ILE A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 485 removed outlier: 3.725A pdb=" N THR A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.731A pdb=" N ARG A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.589A pdb=" N GLY A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.558A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 577 through 595 removed outlier: 4.110A pdb=" N GLN A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.597A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 626 through 642 removed outlier: 3.520A pdb=" N MET A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 removed outlier: 4.071A pdb=" N HIS A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.765A pdb=" N LYS A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 5.430A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 742 through 766 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 776 through 791 removed outlier: 4.818A pdb=" N ILE A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.529A pdb=" N ARG A 796 " --> pdb=" O PRO A 793 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU A 797 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.638A pdb=" N SER A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 818 through 835 removed outlier: 5.622A pdb=" N GLU A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N CYS A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 833 " --> pdb=" O CYS A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 removed outlier: 3.681A pdb=" N GLU A 840 " --> pdb=" O ASP A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 841 through 859 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.666A pdb=" N ALA A 890 " --> pdb=" O MET A 886 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 933 removed outlier: 6.115A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 990 through 1004 removed outlier: 3.634A pdb=" N SER A1003 " --> pdb=" O THR A 999 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1004 " --> pdb=" O GLY A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1027 Processing helix chain 'A' and resid 1030 through 1033 Processing helix chain 'A' and resid 1034 through 1055 removed outlier: 3.530A pdb=" N ARG A1038 " --> pdb=" O PHE A1034 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 435 removed outlier: 3.542A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7347 1.03 - 1.23: 16 1.23 - 1.42: 3064 1.42 - 1.62: 4326 1.62 - 1.81: 82 Bond restraints: 14835 Sorted by residual: bond pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N ILE A 127 " pdb=" H ILE A 127 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" CB PRO A1066 " pdb=" CG PRO A1066 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.18e-01 bond pdb=" N GLU A 227 " pdb=" CA GLU A 227 " ideal model delta sigma weight residual 1.459 1.469 -0.010 1.21e-02 6.83e+03 6.59e-01 bond pdb=" CG LEU A 894 " pdb=" CD2 LEU A 894 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.32e-01 ... (remaining 14830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 25668 1.19 - 2.39: 1140 2.39 - 3.58: 48 3.58 - 4.77: 19 4.77 - 5.96: 3 Bond angle restraints: 26878 Sorted by residual: angle pdb=" N GLU A 227 " pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " ideal model delta sigma weight residual 110.12 113.38 -3.26 1.47e+00 4.63e-01 4.92e+00 angle pdb=" CA TRP A 762 " pdb=" CB TRP A 762 " pdb=" CG TRP A 762 " ideal model delta sigma weight residual 113.60 109.81 3.79 1.90e+00 2.77e-01 3.98e+00 angle pdb=" C LEU A 226 " pdb=" N GLU A 227 " pdb=" CA GLU A 227 " ideal model delta sigma weight residual 120.28 117.66 2.62 1.34e+00 5.57e-01 3.83e+00 angle pdb=" CA PRO A1066 " pdb=" N PRO A1066 " pdb=" CD PRO A1066 " ideal model delta sigma weight residual 112.00 109.53 2.47 1.40e+00 5.10e-01 3.11e+00 angle pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " ideal model delta sigma weight residual 112.70 117.87 -5.17 3.00e+00 1.11e-01 2.97e+00 ... (remaining 26873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 6468 16.90 - 33.81: 354 33.81 - 50.71: 88 50.71 - 67.61: 31 67.61 - 84.52: 12 Dihedral angle restraints: 6953 sinusoidal: 3795 harmonic: 3158 Sorted by residual: dihedral pdb=" CA VAL A 784 " pdb=" C VAL A 784 " pdb=" N LEU A 785 " pdb=" CA LEU A 785 " ideal model delta harmonic sigma weight residual 180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " pdb=" CZ ARG A 231 " ideal model delta sinusoidal sigma weight residual 180.00 135.31 44.69 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA PHE A 838 " pdb=" C PHE A 838 " pdb=" N GLU A 839 " pdb=" CA GLU A 839 " ideal model delta harmonic sigma weight residual 180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 833 0.031 - 0.063: 233 0.063 - 0.094: 69 0.094 - 0.125: 25 0.125 - 0.157: 4 Chirality restraints: 1164 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA ILE A 236 " pdb=" N ILE A 236 " pdb=" C ILE A 236 " pdb=" CB ILE A 236 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL A1056 " pdb=" N VAL A1056 " pdb=" C VAL A1056 " pdb=" CB VAL A1056 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1161 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1065 " -0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A1066 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A1066 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1066 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1025 " -0.000 2.00e-02 2.50e+03 8.15e-03 1.99e+00 pdb=" CG PHE A1025 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A1025 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A1025 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1025 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1025 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A1025 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A1025 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A1025 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A1025 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A1025 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A1025 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 882 " 0.009 2.00e-02 2.50e+03 8.05e-03 1.94e+00 pdb=" CG PHE A 882 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 882 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 882 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 882 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 882 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 882 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 882 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 882 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 882 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 882 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 882 " 0.002 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 984 2.22 - 2.82: 31692 2.82 - 3.41: 40207 3.41 - 4.01: 51431 4.01 - 4.60: 81126 Nonbonded interactions: 205440 Sorted by model distance: nonbonded pdb=" OD1 ASN A 662 " pdb="HE22 GLN A 709 " model vdw 1.628 2.450 nonbonded pdb=" O GLU A 338 " pdb="HH12 ARG A 344 " model vdw 1.636 2.450 nonbonded pdb=" O PHE A1002 " pdb="HD21 ASN A1005 " model vdw 1.657 2.450 nonbonded pdb="HH12 ARG A 887 " pdb=" OE2 GLU A1039 " model vdw 1.672 2.450 nonbonded pdb=" OE2 GLU A 338 " pdb=" HH TYR A 409 " model vdw 1.675 2.450 ... (remaining 205435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 3.050 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: 0.060 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7472 Z= 0.107 Angle : 0.466 5.409 10124 Z= 0.240 Chirality : 0.035 0.157 1164 Planarity : 0.003 0.081 1293 Dihedral : 13.065 84.518 2788 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.65 (0.29), residues: 897 helix: 2.83 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.99 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 845 TYR 0.014 0.001 TYR A 657 PHE 0.021 0.002 PHE A 882 TRP 0.013 0.001 TRP A 762 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7472) covalent geometry : angle 0.46570 (10124) hydrogen bonds : bond 0.15557 ( 531) hydrogen bonds : angle 5.42764 ( 1549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.318 Fit side-chains REVERT: A 168 MET cc_start: 0.9457 (mmp) cc_final: 0.9189 (mmp) REVERT: A 804 MET cc_start: 0.8954 (mmt) cc_final: 0.8481 (mmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.9169 time to fit residues: 45.2749 Evaluate side-chains 41 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 951 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.084686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056944 restraints weight = 56020.224| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.28 r_work: 0.2793 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7472 Z= 0.125 Angle : 0.527 5.771 10124 Z= 0.280 Chirality : 0.036 0.130 1164 Planarity : 0.004 0.063 1293 Dihedral : 3.682 22.504 957 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.12 % Allowed : 3.27 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.60 (0.29), residues: 897 helix: 2.74 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 1.10 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 845 TYR 0.006 0.001 TYR A 551 PHE 0.027 0.002 PHE A 882 TRP 0.014 0.001 TRP A 762 HIS 0.008 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7472) covalent geometry : angle 0.52693 (10124) hydrogen bonds : bond 0.04917 ( 531) hydrogen bonds : angle 4.41746 ( 1549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.9425 (mmp) cc_final: 0.9201 (mmp) REVERT: A 261 ARG cc_start: 0.7543 (ptm160) cc_final: 0.7256 (ttp-110) REVERT: A 804 MET cc_start: 0.8830 (mmt) cc_final: 0.8567 (mmt) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 1.0716 time to fit residues: 51.4893 Evaluate side-chains 43 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.084278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056487 restraints weight = 59621.188| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.36 r_work: 0.2781 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7472 Z= 0.132 Angle : 0.490 5.661 10124 Z= 0.261 Chirality : 0.035 0.131 1164 Planarity : 0.003 0.053 1293 Dihedral : 3.645 20.875 957 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.63 (0.28), residues: 897 helix: 2.76 (0.19), residues: 703 sheet: None (None), residues: 0 loop : 1.10 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.009 0.001 TYR A 657 PHE 0.024 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7472) covalent geometry : angle 0.48999 (10124) hydrogen bonds : bond 0.04517 ( 531) hydrogen bonds : angle 4.23907 ( 1549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9398 (mmp) cc_final: 0.9157 (mmp) REVERT: A 804 MET cc_start: 0.8861 (mmt) cc_final: 0.8529 (mmt) outliers start: 0 outliers final: 1 residues processed: 44 average time/residue: 0.9318 time to fit residues: 44.4965 Evaluate side-chains 44 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.085307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057421 restraints weight = 60575.674| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.41 r_work: 0.2801 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7472 Z= 0.105 Angle : 0.477 7.468 10124 Z= 0.248 Chirality : 0.034 0.128 1164 Planarity : 0.003 0.047 1293 Dihedral : 3.603 21.344 957 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 3.88 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.69 (0.29), residues: 897 helix: 2.85 (0.19), residues: 703 sheet: None (None), residues: 0 loop : 0.93 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.008 0.001 TYR A 551 PHE 0.024 0.001 PHE A 882 TRP 0.014 0.001 TRP A 142 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7472) covalent geometry : angle 0.47688 (10124) hydrogen bonds : bond 0.03948 ( 531) hydrogen bonds : angle 4.05524 ( 1549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9380 (mmp) cc_final: 0.9127 (mmp) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.9078 time to fit residues: 45.3445 Evaluate side-chains 44 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.084282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.056494 restraints weight = 58081.156| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.34 r_work: 0.2771 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7472 Z= 0.151 Angle : 0.495 7.172 10124 Z= 0.259 Chirality : 0.035 0.132 1164 Planarity : 0.003 0.043 1293 Dihedral : 3.621 20.609 957 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.59 (0.28), residues: 897 helix: 2.77 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.92 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 845 TYR 0.012 0.001 TYR A 657 PHE 0.025 0.001 PHE A 882 TRP 0.021 0.001 TRP A 142 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7472) covalent geometry : angle 0.49518 (10124) hydrogen bonds : bond 0.04117 ( 531) hydrogen bonds : angle 4.08115 ( 1549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9376 (mmp) cc_final: 0.9124 (mmp) REVERT: A 445 MET cc_start: 0.7009 (pmm) cc_final: 0.6163 (pmm) REVERT: A 804 MET cc_start: 0.8648 (mmm) cc_final: 0.8446 (mmp) outliers start: 0 outliers final: 1 residues processed: 43 average time/residue: 1.0240 time to fit residues: 47.7203 Evaluate side-chains 44 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.085065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057081 restraints weight = 60810.528| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.42 r_work: 0.2797 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7472 Z= 0.102 Angle : 0.475 7.175 10124 Z= 0.244 Chirality : 0.034 0.128 1164 Planarity : 0.003 0.041 1293 Dihedral : 3.577 20.796 957 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.75 (0.29), residues: 897 helix: 2.88 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.96 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.007 0.001 TYR A 657 PHE 0.024 0.001 PHE A 882 TRP 0.015 0.001 TRP A 142 HIS 0.003 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7472) covalent geometry : angle 0.47494 (10124) hydrogen bonds : bond 0.03798 ( 531) hydrogen bonds : angle 3.95807 ( 1549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7033 (pmm) cc_final: 0.6189 (pmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.9941 time to fit residues: 46.3068 Evaluate side-chains 43 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.084882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057008 restraints weight = 59380.096| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.36 r_work: 0.2802 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7472 Z= 0.113 Angle : 0.480 6.300 10124 Z= 0.246 Chirality : 0.034 0.128 1164 Planarity : 0.003 0.039 1293 Dihedral : 3.560 20.488 957 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.76 (0.28), residues: 897 helix: 2.89 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.96 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.009 0.001 TYR A 657 PHE 0.024 0.001 PHE A 882 TRP 0.014 0.001 TRP A 142 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7472) covalent geometry : angle 0.48040 (10124) hydrogen bonds : bond 0.03763 ( 531) hydrogen bonds : angle 3.93366 ( 1549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7073 (pmm) cc_final: 0.6236 (pmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.9950 time to fit residues: 46.3184 Evaluate side-chains 42 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.083721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055656 restraints weight = 65219.505| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.49 r_work: 0.2754 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7472 Z= 0.153 Angle : 0.503 7.286 10124 Z= 0.259 Chirality : 0.036 0.135 1164 Planarity : 0.003 0.040 1293 Dihedral : 3.601 20.348 957 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.63 (0.28), residues: 897 helix: 2.81 (0.19), residues: 705 sheet: None (None), residues: 0 loop : 0.84 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 845 TYR 0.013 0.001 TYR A 657 PHE 0.024 0.001 PHE A 882 TRP 0.013 0.001 TRP A 142 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7472) covalent geometry : angle 0.50276 (10124) hydrogen bonds : bond 0.03989 ( 531) hydrogen bonds : angle 3.98102 ( 1549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7462 (mpt) cc_final: 0.7226 (mpt) REVERT: A 445 MET cc_start: 0.7143 (pmm) cc_final: 0.6310 (pmm) outliers start: 0 outliers final: 1 residues processed: 45 average time/residue: 0.9886 time to fit residues: 48.2289 Evaluate side-chains 45 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.083956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055933 restraints weight = 65009.664| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.48 r_work: 0.2772 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7472 Z= 0.133 Angle : 0.505 9.585 10124 Z= 0.258 Chirality : 0.035 0.129 1164 Planarity : 0.003 0.039 1293 Dihedral : 3.596 20.481 957 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.65 (0.28), residues: 897 helix: 2.83 (0.19), residues: 705 sheet: None (None), residues: 0 loop : 0.85 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 845 TYR 0.010 0.001 TYR A 657 PHE 0.029 0.001 PHE A1025 TRP 0.023 0.001 TRP A 142 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7472) covalent geometry : angle 0.50529 (10124) hydrogen bonds : bond 0.03916 ( 531) hydrogen bonds : angle 3.94089 ( 1549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7154 (pmm) cc_final: 0.6334 (pmm) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.9979 time to fit residues: 47.5569 Evaluate side-chains 44 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.084309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056300 restraints weight = 63516.546| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.46 r_work: 0.2768 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7472 Z= 0.122 Angle : 0.504 10.802 10124 Z= 0.256 Chirality : 0.035 0.127 1164 Planarity : 0.003 0.039 1293 Dihedral : 3.583 20.462 957 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.69 (0.28), residues: 897 helix: 2.86 (0.19), residues: 705 sheet: None (None), residues: 0 loop : 0.83 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 845 TYR 0.010 0.001 TYR A 657 PHE 0.024 0.001 PHE A 882 TRP 0.029 0.001 TRP A 142 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7472) covalent geometry : angle 0.50434 (10124) hydrogen bonds : bond 0.03812 ( 531) hydrogen bonds : angle 3.90438 ( 1549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7619 (ptm160) cc_final: 0.6955 (ttp-110) outliers start: 1 outliers final: 2 residues processed: 44 average time/residue: 1.0675 time to fit residues: 50.2933 Evaluate side-chains 45 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4054 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.085469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057862 restraints weight = 56369.779| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.29 r_work: 0.2814 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7472 Z= 0.097 Angle : 0.500 10.725 10124 Z= 0.249 Chirality : 0.034 0.132 1164 Planarity : 0.003 0.039 1293 Dihedral : 3.525 20.367 957 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.36 % Allowed : 5.58 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.84 (0.28), residues: 897 helix: 2.96 (0.19), residues: 705 sheet: None (None), residues: 0 loop : 0.92 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.006 0.001 TYR A 551 PHE 0.024 0.001 PHE A 882 TRP 0.027 0.001 TRP A 142 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7472) covalent geometry : angle 0.50049 (10124) hydrogen bonds : bond 0.03480 ( 531) hydrogen bonds : angle 3.79982 ( 1549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4325.72 seconds wall clock time: 74 minutes 12.25 seconds (4452.25 seconds total)