Starting phenix.real_space_refine on Thu Jul 2 06:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391.map" model { file = "/net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cah_45391/07_2026/9cah_45391_neut.cif" } resolution = 3.16 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 3 6.06 5 S 52 5.16 5 C 4487 2.51 5 N 1239 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5683 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 40, 'TRANS': 677} Chain: "B" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1429 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 3 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5599 SG CYS A 706 41.630 26.784 46.049 1.00105.08 S ATOM 5622 SG CYS A 709 38.223 28.296 47.032 1.00107.63 S ATOM 5658 SG CYS A 714 41.003 29.955 43.810 1.00105.86 S ATOM 4933 SG CYS A 624 52.715 35.645 54.988 1.00 75.17 S ATOM 4952 SG CYS A 627 54.629 38.550 56.667 1.00 72.52 S ATOM 5092 SG CYS A 643 55.773 34.858 57.070 1.00 67.02 S ATOM 5114 SG CYS A 646 52.796 36.210 58.846 1.00 68.39 S ATOM 5279 SG CYS A 666 43.263 32.681 47.203 1.00 86.48 S ATOM 5452 SG CYS A 688 45.031 30.280 49.793 1.00 84.08 S ATOM 5477 SG CYS A 691 42.145 30.469 50.411 1.00 85.61 S Time building chain proxies: 1.10, per 1000 atoms: 0.15 Number of scatterers: 7116 At special positions: 0 Unit cell: (73.04, 102.92, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Mn 1 24.99 S 52 16.00 O 1334 8.00 N 1239 7.00 C 4487 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: 0.56 Conformation dependent library (CDL) restraints added in 311.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 706 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 714 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 709 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 646 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 643 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 627 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 624 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 666 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 691 " Number of angles added : 6 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 38.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.711A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 171 through 200 removed outlier: 3.930A pdb=" N CYS A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.659A pdb=" N PHE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.674A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 573 Processing helix chain 'A' and resid 577 through 599 Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.806A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.803A pdb=" N ASN A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.588A pdb=" N GLU A 708 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 709 " --> pdb=" O CYS A 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 705 through 709' Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.625A pdb=" N ASN B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 162 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.289A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 41 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 248 removed outlier: 7.557A pdb=" N LEU A 243 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 16.193A pdb=" N SER A 254 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 13.848A pdb=" N LYS A 445 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LEU A 256 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER A 443 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 291 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 623 removed outlier: 3.661A pdb=" N LYS A 619 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 631 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 643 removed outlier: 4.016A pdb=" N GLU A 648 " --> pdb=" O CYS A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 657 through 660 removed outlier: 3.806A pdb=" N TYR A 685 " --> pdb=" O TRP A 676 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 142 removed outlier: 9.589A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 822 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: 1.07 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2351 1.35 - 1.46: 1561 1.46 - 1.58: 3282 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 7271 Sorted by residual: bond pdb=" N GLU A 663 " pdb=" CA GLU A 663 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.99e+00 bond pdb=" N ASP A 669 " pdb=" CA ASP A 669 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.42e-02 4.96e+03 6.96e+00 bond pdb=" N GLU A 9 " pdb=" CA GLU A 9 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.77e+00 bond pdb=" N LEU A 606 " pdb=" CA LEU A 606 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.33e-02 5.65e+03 5.65e+00 bond pdb=" N LYS A 702 " pdb=" CA LYS A 702 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.22e-02 6.72e+03 5.37e+00 ... (remaining 7266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 9510 1.45 - 2.90: 245 2.90 - 4.34: 67 4.34 - 5.79: 10 5.79 - 7.24: 5 Bond angle restraints: 9837 Sorted by residual: angle pdb=" CA LYS A 662 " pdb=" C LYS A 662 " pdb=" O LYS A 662 " ideal model delta sigma weight residual 121.28 117.25 4.03 1.19e+00 7.06e-01 1.14e+01 angle pdb=" N ASP A 604 " pdb=" CA ASP A 604 " pdb=" C ASP A 604 " ideal model delta sigma weight residual 111.71 108.19 3.52 1.15e+00 7.56e-01 9.34e+00 angle pdb=" CA SER A 713 " pdb=" C SER A 713 " pdb=" O SER A 713 " ideal model delta sigma weight residual 121.50 117.77 3.73 1.25e+00 6.40e-01 8.90e+00 angle pdb=" C ASP A 117 " pdb=" CA ASP A 117 " pdb=" CB ASP A 117 " ideal model delta sigma weight residual 109.72 114.63 -4.91 1.66e+00 3.63e-01 8.75e+00 angle pdb=" CA GLU A 605 " pdb=" C GLU A 605 " pdb=" O GLU A 605 " ideal model delta sigma weight residual 120.82 117.72 3.10 1.05e+00 9.07e-01 8.73e+00 ... (remaining 9832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3941 17.98 - 35.96: 394 35.96 - 53.94: 65 53.94 - 71.92: 15 71.92 - 89.90: 8 Dihedral angle restraints: 4423 sinusoidal: 1802 harmonic: 2621 Sorted by residual: dihedral pdb=" CA VAL B 154 " pdb=" C VAL B 154 " pdb=" N GLU B 155 " pdb=" CA GLU B 155 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA MET A 276 " pdb=" C MET A 276 " pdb=" N THR A 277 " pdb=" CA THR A 277 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" N LYS A 90 " pdb=" CA LYS A 90 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 743 0.035 - 0.070: 245 0.070 - 0.105: 71 0.105 - 0.140: 23 0.140 - 0.175: 1 Chirality restraints: 1083 Sorted by residual: chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CG LEU A 570 " pdb=" CB LEU A 570 " pdb=" CD1 LEU A 570 " pdb=" CD2 LEU A 570 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA VAL A 4 " pdb=" N VAL A 4 " pdb=" C VAL A 4 " pdb=" CB VAL A 4 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1080 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 660 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C LEU A 660 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU A 660 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 661 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C THR A 158 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 159 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 161 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C TRP B 161 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP B 161 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 162 " 0.012 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 64 2.62 - 3.19: 6105 3.19 - 3.76: 10609 3.76 - 4.33: 14364 4.33 - 4.90: 23997 Nonbonded interactions: 55139 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 801 " model vdw 2.049 3.060 nonbonded pdb=" OD2 ASP A 669 " pdb="ZN ZN A 804 " model vdw 2.091 2.230 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 801 " model vdw 2.141 3.060 nonbonded pdb=" OE1 GLN A 196 " pdb=" OH TYR A 548 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 510 " pdb=" OE2 GLU A 565 " model vdw 2.206 3.040 ... (remaining 55134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.184 7281 Z= 0.195 Angle : 0.619 7.238 9843 Z= 0.341 Chirality : 0.040 0.175 1083 Planarity : 0.004 0.048 1276 Dihedral : 14.902 89.896 2735 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 0.13 % Allowed : 0.25 % Favored : 99.62 % 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: -0.12 (0.28), residues: 903 helix: 1.22 (0.30), residues: 314 sheet: -0.22 (0.45), residues: 140 loop : -0.96 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 665 TYR 0.014 0.001 TYR A 411 PHE 0.010 0.001 PHE A 235 TRP 0.011 0.001 TRP B 161 HIS 0.003 0.000 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 ( 7271) covalent geometry : angle 0.61313 / 0.34 ( 9837) hydrogen bonds : bond 0.12100 / 8.31 ( 288) hydrogen bonds : angle 5.15066 / 3.64 ( 822) metal coordination : bond 0.08673 / 8.24 ( 10) metal coordination : angle 3.42518 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.259 Fit side-chains REVERT: A 164 MET cc_start: 0.7683 (tpp) cc_final: 0.7328 (tpt) REVERT: A 166 CYS cc_start: 0.7043 (p) cc_final: 0.6721 (p) REVERT: A 281 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7976 (ptpp) REVERT: A 357 GLN cc_start: 0.8171 (mt0) cc_final: 0.7863 (mt0) REVERT: A 552 ASP cc_start: 0.7177 (t0) cc_final: 0.6911 (t0) REVERT: A 632 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7964 (mttm) REVERT: A 662 LYS cc_start: 0.8079 (mttt) cc_final: 0.7651 (mtmt) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.0867 time to fit residues: 21.6518 Evaluate side-chains 175 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A 218 GLN A 382 HIS A 517 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108474 restraints weight = 10627.856| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.12 r_work: 0.3246 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7281 Z= 0.123 Angle : 0.604 8.678 9843 Z= 0.299 Chirality : 0.041 0.145 1083 Planarity : 0.004 0.056 1276 Dihedral : 4.292 18.555 977 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.27 % Allowed : 10.67 % Favored : 88.06 % 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: 0.07 (0.29), residues: 903 helix: 1.44 (0.30), residues: 311 sheet: -0.24 (0.45), residues: 141 loop : -0.83 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.012 0.001 TYR A 411 PHE 0.009 0.001 PHE A 596 TRP 0.010 0.001 TRP B 14 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7271) covalent geometry : angle 0.59277 / 0.30 ( 9837) hydrogen bonds : bond 0.04172 / 2.92 ( 288) hydrogen bonds : angle 4.41322 / 3.10 ( 822) metal coordination : bond 0.00403 / 0.30 ( 10) metal coordination : angle 4.71476 / 3.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.267 Fit side-chains REVERT: A 145 LYS cc_start: 0.8540 (tttt) cc_final: 0.8312 (tttm) REVERT: A 164 MET cc_start: 0.7886 (tpp) cc_final: 0.7685 (tpt) REVERT: A 198 LYS cc_start: 0.8298 (tptp) cc_final: 0.8076 (tptm) REVERT: A 281 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8292 (ptpp) REVERT: A 357 GLN cc_start: 0.8339 (mt0) cc_final: 0.7919 (mt0) REVERT: A 376 ASN cc_start: 0.7821 (t0) cc_final: 0.7525 (t0) REVERT: A 433 PHE cc_start: 0.8498 (m-80) cc_final: 0.8210 (m-80) REVERT: A 552 ASP cc_start: 0.7841 (t0) cc_final: 0.7616 (t0) REVERT: A 659 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7820 (ttmm) REVERT: A 662 LYS cc_start: 0.8613 (mttt) cc_final: 0.8231 (mtmt) outliers start: 10 outliers final: 6 residues processed: 182 average time/residue: 0.1003 time to fit residues: 22.7902 Evaluate side-chains 180 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104888 restraints weight = 10538.735| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7281 Z= 0.162 Angle : 0.606 9.357 9843 Z= 0.298 Chirality : 0.041 0.148 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.326 17.682 977 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.80 % Allowed : 12.45 % Favored : 84.75 % 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: 0.10 (0.29), residues: 903 helix: 1.48 (0.30), residues: 311 sheet: -0.28 (0.45), residues: 142 loop : -0.82 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.012 0.001 TYR A 411 PHE 0.017 0.001 PHE A 127 TRP 0.010 0.001 TRP B 14 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 7271) covalent geometry : angle 0.59165 / 0.30 ( 9837) hydrogen bonds : bond 0.04270 / 2.96 ( 288) hydrogen bonds : angle 4.40169 / 3.10 ( 822) metal coordination : bond 0.00581 / 0.52 ( 10) metal coordination : angle 5.33352 / 3.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.269 Fit side-chains REVERT: A 281 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8299 (ptpp) REVERT: A 357 GLN cc_start: 0.8352 (mt0) cc_final: 0.8063 (mt0) REVERT: A 376 ASN cc_start: 0.7952 (t0) cc_final: 0.7649 (t0) REVERT: A 552 ASP cc_start: 0.7872 (t0) cc_final: 0.7670 (t0) REVERT: A 662 LYS cc_start: 0.8623 (mttt) cc_final: 0.8307 (mtmt) REVERT: A 665 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7660 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 0.0985 time to fit residues: 23.4374 Evaluate side-chains 194 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 48 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 chunk 19 optimal weight: 0.5980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105560 restraints weight = 10606.525| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.11 r_work: 0.3209 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7281 Z= 0.122 Angle : 0.583 9.225 9843 Z= 0.287 Chirality : 0.040 0.138 1083 Planarity : 0.004 0.041 1276 Dihedral : 4.310 18.200 977 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.29 % Allowed : 15.12 % Favored : 82.59 % 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: 0.12 (0.29), residues: 903 helix: 1.49 (0.30), residues: 311 sheet: -0.31 (0.45), residues: 141 loop : -0.77 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.013 0.001 TYR A 411 PHE 0.015 0.001 PHE A 127 TRP 0.009 0.001 TRP B 14 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7271) covalent geometry : angle 0.57029 / 0.29 ( 9837) hydrogen bonds : bond 0.03984 / 2.77 ( 288) hydrogen bonds : angle 4.30993 / 3.03 ( 822) metal coordination : bond 0.00383 / 0.31 ( 10) metal coordination : angle 4.89871 / 3.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.195 Fit side-chains REVERT: A 23 ARG cc_start: 0.7964 (mpt-90) cc_final: 0.7666 (mpt-90) REVERT: A 145 LYS cc_start: 0.8607 (tttt) cc_final: 0.8363 (tttm) REVERT: A 185 ASP cc_start: 0.7501 (m-30) cc_final: 0.7300 (m-30) REVERT: A 281 LYS cc_start: 0.8526 (ptpt) cc_final: 0.8315 (ptpp) REVERT: A 331 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8459 (mt0) REVERT: A 357 GLN cc_start: 0.8297 (mt0) cc_final: 0.8029 (mt0) REVERT: A 376 ASN cc_start: 0.7827 (t0) cc_final: 0.7555 (t0) REVERT: A 662 LYS cc_start: 0.8645 (mttt) cc_final: 0.8294 (mtmt) outliers start: 18 outliers final: 11 residues processed: 187 average time/residue: 0.0925 time to fit residues: 21.6281 Evaluate side-chains 192 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103210 restraints weight = 10690.795| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.08 r_work: 0.3175 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7281 Z= 0.227 Angle : 0.650 10.279 9843 Z= 0.322 Chirality : 0.044 0.155 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.494 18.340 977 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.30 % Allowed : 15.76 % Favored : 80.94 % 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: -0.04 (0.28), residues: 903 helix: 1.28 (0.30), residues: 314 sheet: -0.42 (0.41), residues: 153 loop : -0.82 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.013 0.002 TYR A 578 PHE 0.018 0.002 PHE A 127 TRP 0.014 0.002 TRP B 14 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 ( 7271) covalent geometry : angle 0.63388 / 0.32 ( 9837) hydrogen bonds : bond 0.04684 / 3.25 ( 288) hydrogen bonds : angle 4.48698 / 3.16 ( 822) metal coordination : bond 0.00534 / 0.43 ( 10) metal coordination : angle 5.90073 / 4.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.268 Fit side-chains REVERT: A 96 LEU cc_start: 0.8418 (mt) cc_final: 0.8110 (mt) REVERT: A 145 LYS cc_start: 0.8644 (tttt) cc_final: 0.8403 (tttp) REVERT: A 185 ASP cc_start: 0.7545 (m-30) cc_final: 0.7304 (m-30) REVERT: A 331 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: A 376 ASN cc_start: 0.7928 (t0) cc_final: 0.7638 (t0) REVERT: A 659 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7997 (mtmm) REVERT: A 662 LYS cc_start: 0.8644 (mttt) cc_final: 0.8274 (mtmt) outliers start: 26 outliers final: 19 residues processed: 200 average time/residue: 0.0948 time to fit residues: 23.8451 Evaluate side-chains 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.0020 chunk 84 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104319 restraints weight = 10626.367| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.10 r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7281 Z= 0.138 Angle : 0.602 10.096 9843 Z= 0.299 Chirality : 0.041 0.142 1083 Planarity : 0.004 0.041 1276 Dihedral : 4.405 18.128 977 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.18 % Allowed : 17.41 % Favored : 79.42 % 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: 0.05 (0.29), residues: 903 helix: 1.38 (0.30), residues: 318 sheet: -0.36 (0.42), residues: 153 loop : -0.82 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 665 TYR 0.013 0.001 TYR A 411 PHE 0.016 0.001 PHE A 127 TRP 0.011 0.001 TRP B 14 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7271) covalent geometry : angle 0.58922 / 0.30 ( 9837) hydrogen bonds : bond 0.04203 / 2.92 ( 288) hydrogen bonds : angle 4.36516 / 3.09 ( 822) metal coordination : bond 0.00360 / 0.28 ( 10) metal coordination : angle 5.08962 / 3.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.262 Fit side-chains REVERT: A 6 MET cc_start: 0.8024 (mtt) cc_final: 0.7695 (mtt) REVERT: A 23 ARG cc_start: 0.8020 (mpt-90) cc_final: 0.7729 (mpt-90) REVERT: A 145 LYS cc_start: 0.8609 (tttt) cc_final: 0.8360 (tttp) REVERT: A 185 ASP cc_start: 0.7560 (m-30) cc_final: 0.7289 (m-30) REVERT: A 331 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: A 376 ASN cc_start: 0.7844 (t0) cc_final: 0.7567 (t0) REVERT: A 659 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7930 (mtmm) REVERT: A 662 LYS cc_start: 0.8630 (mttt) cc_final: 0.8249 (mtmt) outliers start: 25 outliers final: 16 residues processed: 188 average time/residue: 0.0964 time to fit residues: 22.6503 Evaluate side-chains 193 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.0370 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103989 restraints weight = 10589.246| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.09 r_work: 0.3191 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7281 Z= 0.160 Angle : 0.609 10.179 9843 Z= 0.302 Chirality : 0.041 0.143 1083 Planarity : 0.004 0.040 1276 Dihedral : 4.378 18.182 977 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.43 % Allowed : 18.04 % Favored : 78.53 % 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: 0.03 (0.29), residues: 903 helix: 1.36 (0.30), residues: 319 sheet: -0.39 (0.42), residues: 153 loop : -0.81 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.012 0.001 TYR A 41 PHE 0.017 0.001 PHE A 127 TRP 0.012 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 7271) covalent geometry : angle 0.59567 / 0.30 ( 9837) hydrogen bonds : bond 0.04281 / 2.98 ( 288) hydrogen bonds : angle 4.34372 / 3.06 ( 822) metal coordination : bond 0.00386 / 0.30 ( 10) metal coordination : angle 5.12680 / 3.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.295 Fit side-chains REVERT: A 6 MET cc_start: 0.8052 (mtt) cc_final: 0.7743 (mtt) REVERT: A 23 ARG cc_start: 0.8030 (mpt-90) cc_final: 0.7722 (mpt-90) REVERT: A 145 LYS cc_start: 0.8638 (tttt) cc_final: 0.8404 (tttp) REVERT: A 185 ASP cc_start: 0.7604 (m-30) cc_final: 0.7335 (m-30) REVERT: A 331 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: A 376 ASN cc_start: 0.7880 (t0) cc_final: 0.7591 (t0) REVERT: A 377 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: A 659 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7961 (mtmm) REVERT: A 662 LYS cc_start: 0.8612 (mttt) cc_final: 0.8191 (mtmt) REVERT: B 160 LYS cc_start: 0.8557 (mptt) cc_final: 0.8240 (mptt) outliers start: 27 outliers final: 17 residues processed: 189 average time/residue: 0.0946 time to fit residues: 22.7651 Evaluate side-chains 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103053 restraints weight = 10741.319| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.10 r_work: 0.3169 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7281 Z= 0.197 Angle : 0.634 10.614 9843 Z= 0.316 Chirality : 0.043 0.145 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.466 18.166 977 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.05 % Allowed : 18.93 % Favored : 78.02 % 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: -0.06 (0.28), residues: 903 helix: 1.25 (0.29), residues: 320 sheet: -0.38 (0.42), residues: 153 loop : -0.88 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.012 0.001 TYR A 578 PHE 0.017 0.002 PHE A 127 TRP 0.014 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 7271) covalent geometry : angle 0.62007 / 0.31 ( 9837) hydrogen bonds : bond 0.04527 / 3.16 ( 288) hydrogen bonds : angle 4.42266 / 3.13 ( 822) metal coordination : bond 0.00425 / 0.33 ( 10) metal coordination : angle 5.45378 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.278 Fit side-chains REVERT: A 6 MET cc_start: 0.8146 (mtt) cc_final: 0.7850 (mtt) REVERT: A 23 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7729 (mpt-90) REVERT: A 145 LYS cc_start: 0.8654 (tttt) cc_final: 0.8418 (tttp) REVERT: A 185 ASP cc_start: 0.7630 (m-30) cc_final: 0.7362 (m-30) REVERT: A 331 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: A 376 ASN cc_start: 0.7887 (t0) cc_final: 0.7603 (t0) REVERT: A 377 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7940 (mmm-85) REVERT: A 659 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7991 (mtmm) REVERT: A 662 LYS cc_start: 0.8613 (mttt) cc_final: 0.8084 (mtmt) REVERT: A 663 GLU cc_start: 0.8477 (mp0) cc_final: 0.7938 (mp0) REVERT: B 160 LYS cc_start: 0.8572 (mptt) cc_final: 0.8258 (mptt) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.1066 time to fit residues: 24.9144 Evaluate side-chains 202 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105147 restraints weight = 10608.901| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.11 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7281 Z= 0.118 Angle : 0.588 10.223 9843 Z= 0.294 Chirality : 0.040 0.143 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.353 17.771 977 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.54 % Allowed : 19.19 % Favored : 78.27 % 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: 0.08 (0.29), residues: 903 helix: 1.39 (0.30), residues: 318 sheet: -0.24 (0.43), residues: 146 loop : -0.82 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 377 TYR 0.013 0.001 TYR A 411 PHE 0.015 0.001 PHE A 127 TRP 0.011 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7271) covalent geometry : angle 0.57727 / 0.29 ( 9837) hydrogen bonds : bond 0.04050 / 2.83 ( 288) hydrogen bonds : angle 4.29204 / 3.04 ( 822) metal coordination : bond 0.00297 / 0.22 ( 10) metal coordination : angle 4.66374 / 3.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.193 Fit side-chains REVERT: A 6 MET cc_start: 0.8062 (mtt) cc_final: 0.7749 (mtt) REVERT: A 23 ARG cc_start: 0.8012 (mpt-90) cc_final: 0.7797 (mpp80) REVERT: A 145 LYS cc_start: 0.8574 (tttt) cc_final: 0.8331 (tttp) REVERT: A 185 ASP cc_start: 0.7625 (m-30) cc_final: 0.7345 (m-30) REVERT: A 331 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: A 376 ASN cc_start: 0.7817 (t0) cc_final: 0.7537 (t0) REVERT: A 500 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7820 (mt) REVERT: A 552 ASP cc_start: 0.7464 (t0) cc_final: 0.7235 (t70) REVERT: A 659 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7962 (mtmm) REVERT: A 662 LYS cc_start: 0.8610 (mttt) cc_final: 0.8060 (mtmt) REVERT: A 663 GLU cc_start: 0.8499 (mp0) cc_final: 0.7977 (mp0) REVERT: B 160 LYS cc_start: 0.8533 (mptt) cc_final: 0.8213 (mptt) outliers start: 20 outliers final: 16 residues processed: 189 average time/residue: 0.0941 time to fit residues: 22.4470 Evaluate side-chains 197 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 37 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104697 restraints weight = 10594.491| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.11 r_work: 0.3205 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7281 Z= 0.133 Angle : 0.603 10.214 9843 Z= 0.301 Chirality : 0.041 0.182 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.318 18.974 977 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.54 % Allowed : 19.57 % Favored : 77.89 % 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: 0.08 (0.29), residues: 903 helix: 1.38 (0.30), residues: 319 sheet: -0.25 (0.43), residues: 146 loop : -0.81 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.013 0.001 TYR A 411 PHE 0.017 0.001 PHE A 127 TRP 0.013 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 7271) covalent geometry : angle 0.59142 / 0.30 ( 9837) hydrogen bonds : bond 0.04101 / 2.86 ( 288) hydrogen bonds : angle 4.30390 / 3.03 ( 822) metal coordination : bond 0.00321 / 0.25 ( 10) metal coordination : angle 4.83442 / 3.44 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.167 Fit side-chains REVERT: A 6 MET cc_start: 0.8059 (mtt) cc_final: 0.7761 (mtt) REVERT: A 23 ARG cc_start: 0.7992 (mpt-90) cc_final: 0.7779 (mpp80) REVERT: A 145 LYS cc_start: 0.8610 (tttt) cc_final: 0.8356 (tttp) REVERT: A 185 ASP cc_start: 0.7628 (m-30) cc_final: 0.7330 (m-30) REVERT: A 376 ASN cc_start: 0.7820 (t0) cc_final: 0.7549 (t0) REVERT: A 659 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7979 (mtmm) REVERT: A 662 LYS cc_start: 0.8609 (mttt) cc_final: 0.8062 (mtmt) REVERT: A 663 GLU cc_start: 0.8481 (mp0) cc_final: 0.7955 (mp0) REVERT: B 160 LYS cc_start: 0.8531 (mptt) cc_final: 0.8216 (mptt) outliers start: 20 outliers final: 17 residues processed: 182 average time/residue: 0.0959 time to fit residues: 21.7340 Evaluate side-chains 191 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.0170 chunk 29 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103568 restraints weight = 10648.046| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7281 Z= 0.172 Angle : 0.631 10.301 9843 Z= 0.314 Chirality : 0.042 0.143 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.400 17.975 977 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.16 % Allowed : 19.70 % Favored : 78.14 % 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: -0.00 (0.29), residues: 903 helix: 1.29 (0.30), residues: 320 sheet: -0.37 (0.42), residues: 153 loop : -0.82 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.012 0.001 TYR A 411 PHE 0.018 0.002 PHE A 127 TRP 0.015 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 7271) covalent geometry : angle 0.61826 / 0.31 ( 9837) hydrogen bonds : bond 0.04416 / 3.08 ( 288) hydrogen bonds : angle 4.38814 / 3.10 ( 822) metal coordination : bond 0.00375 / 0.29 ( 10) metal coordination : angle 5.16118 / 3.65 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.90 seconds wall clock time: 31 minutes 4.85 seconds (1864.85 seconds total)