Starting phenix.real_space_refine on Wed Sep 17 08:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cah_45391/09_2025/9cah_45391_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cah_45391/09_2025/9cah_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_45391/09_2025/9cah_45391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cah_45391/09_2025/9cah_45391.map" model { file = "/net/cci-nas-00/data/ceres_data/9cah_45391/09_2025/9cah_45391_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cah_45391/09_2025/9cah_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 4 Unusual residues: {' MN': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1.82, per 1000 atoms: 0.26 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: 0.58 Conformation dependent library (CDL) restraints added in 301.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.92 Time building geometry restraints manager: 0.80 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 2.320 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 2.320 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 aren 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 covalent geometry : bond 0.00283 ( 7271) covalent geometry : angle 0.61313 ( 9837) hydrogen bonds : bond 0.12100 ( 288) hydrogen bonds : angle 5.15066 ( 822) metal coordination : bond 0.08673 ( 10) metal coordination : angle 3.42518 ( 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 : 0.287 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: 0.8197 (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: 0.1111 time to fit residues: 27.2463 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 : 0.186 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3574 r_free = 0.3574 target = 0.122867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108069 restraints weight = 10615.964| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.13 r_work: 0.3245 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: 0.7835 moved from start: 0.0961 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= 0.122 Angle : 0.601 8.592 9843 Z= 0.297 Chirality : 0.041 0.143 1083 Planarity : 0.004 0.053 1276 Dihedral : 4.294 18.534 977 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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 aren not related in a simple way. whole: 0.07 (0.29), residues: 903 helix: 1.43 (0.30), residues: 311 sheet: -0.25 (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 0.013 0.001 TYR A 685 PHE 0.009 0.001 PHE A 596 TRP 0.009 0.001 TRP B 14 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7271) covalent geometry : angle 0.58923 ( 9837) hydrogen bonds : bond 0.04164 ( 288) hydrogen bonds : angle 4.40576 ( 822) metal coordination : bond 0.00455 ( 10) metal coordination : angle 4.84866 ( 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 187 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.218 Fit side-chains REVERT: A 51 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7493 (ttp80) REVERT: A 145 LYS cc_start: 0.8537 (tttt) cc_final: 0.8305 (tttm) REVERT: A 198 LYS cc_start: 0.8296 (tptp) cc_final: 0.8074 (tptm) REVERT: A 281 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8292 (ptpp) REVERT: A 376 ASN cc_start: 0.7814 (t0) cc_final: 0.7546 (t0) REVERT: A 433 PHE cc_start: 0.8502 (m-80) cc_final: 0.8207 (m-80) REVERT: A 552 ASP cc_start: 0.7848 (t0) cc_final: 0.7625 (t0) REVERT: A 662 LYS cc_start: 0.8617 (mttt) cc_final: 0.8233 (mtmt) outliers start: 10 outliers final: 6 residues processed: 179 average time/residue: 0.1253 time to fit residues: 27.8494 Evaluate side-chains 179 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 2.9990 chunk 78 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.119765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104999 restraints weight = 10504.707| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.10 r_work: 0.3203 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7281 Z= 0.160 Angle : 0.605 9.233 9843 Z= 0.299 Chirality : 0.042 0.149 1083 Planarity : 0.004 0.044 1276 Dihedral : 4.343 17.644 977 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.67 % Allowed : 13.09 % Favored : 84.24 % 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 aren not related in a simple way. whole: 0.09 (0.29), residues: 903 helix: 1.48 (0.30), residues: 311 sheet: -0.30 (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 A 524 TYR 0.012 0.001 TYR A 411 PHE 0.017 0.001 PHE A 127 TRP 0.009 0.001 TRP B 14 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7271) covalent geometry : angle 0.59104 ( 9837) hydrogen bonds : bond 0.04292 ( 288) hydrogen bonds : angle 4.40769 ( 822) metal coordination : bond 0.00591 ( 10) metal coordination : angle 5.35989 ( 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 205 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.269 Fit side-chains REVERT: A 145 LYS cc_start: 0.8627 (tttt) cc_final: 0.8420 (tttp) REVERT: A 281 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8296 (ptpp) REVERT: A 357 GLN cc_start: 0.8329 (mt0) cc_final: 0.8013 (mt0) REVERT: A 376 ASN cc_start: 0.7940 (t0) cc_final: 0.7640 (t0) REVERT: A 662 LYS cc_start: 0.8613 (mttt) cc_final: 0.8312 (mtmt) REVERT: A 665 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7683 (ttm-80) outliers start: 21 outliers final: 12 residues processed: 189 average time/residue: 0.1128 time to fit residues: 26.7963 Evaluate side-chains 191 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 687 LEU 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: 0.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0170 chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104975 restraints weight = 10624.257| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.11 r_work: 0.3203 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7281 Z= 0.144 Angle : 0.595 9.589 9843 Z= 0.294 Chirality : 0.041 0.142 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.337 18.409 977 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.54 % Allowed : 15.25 % Favored : 82.21 % 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 aren not related in a simple way. whole: 0.07 (0.29), residues: 903 helix: 1.43 (0.30), residues: 311 sheet: -0.33 (0.45), residues: 142 loop : -0.79 (0.30), residues: 450 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 0.016 0.001 PHE A 127 TRP 0.011 0.001 TRP B 14 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7271) covalent geometry : angle 0.58172 ( 9837) hydrogen bonds : bond 0.04160 ( 288) hydrogen bonds : angle 4.35278 ( 822) metal coordination : bond 0.00415 ( 10) metal coordination : angle 5.16696 ( 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 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.256 Fit side-chains REVERT: A 23 ARG cc_start: 0.7974 (mpt-90) cc_final: 0.7628 (mpt-90) REVERT: A 145 LYS cc_start: 0.8636 (tttt) cc_final: 0.8396 (tttm) REVERT: A 281 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8317 (ptpp) REVERT: A 322 MET cc_start: 0.8374 (tpp) cc_final: 0.8084 (tpt) REVERT: A 331 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: A 357 GLN cc_start: 0.8324 (mt0) cc_final: 0.8050 (mt0) REVERT: A 376 ASN cc_start: 0.7854 (t0) cc_final: 0.7548 (t0) REVERT: A 662 LYS cc_start: 0.8624 (mttt) cc_final: 0.8276 (mtmt) outliers start: 20 outliers final: 13 residues processed: 189 average time/residue: 0.1217 time to fit residues: 28.3303 Evaluate side-chains 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 570 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 0.0980 chunk 51 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.118919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104191 restraints weight = 10669.687| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.10 r_work: 0.3179 rms_B_bonded: 2.51 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: 0.7889 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7281 Z= 0.160 Angle : 0.601 9.758 9843 Z= 0.298 Chirality : 0.042 0.145 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.354 18.278 977 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.05 % Allowed : 15.63 % Favored : 81.32 % 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 aren not related in a simple way. whole: 0.05 (0.28), residues: 903 helix: 1.43 (0.30), residues: 310 sheet: -0.41 (0.44), residues: 142 loop : -0.78 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.012 0.001 TYR A 411 PHE 0.017 0.001 PHE A 127 TRP 0.012 0.001 TRP B 14 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7271) covalent geometry : angle 0.58673 ( 9837) hydrogen bonds : bond 0.04285 ( 288) hydrogen bonds : angle 4.37949 ( 822) metal coordination : bond 0.00433 ( 10) metal coordination : angle 5.26281 ( 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 208 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.278 Fit side-chains REVERT: A 145 LYS cc_start: 0.8636 (tttt) cc_final: 0.8386 (tttp) REVERT: A 281 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8325 (ptpp) REVERT: A 322 MET cc_start: 0.8381 (tpp) cc_final: 0.8090 (tpt) REVERT: A 331 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: A 376 ASN cc_start: 0.7849 (t0) cc_final: 0.7581 (t0) REVERT: A 659 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7844 (mtpp) REVERT: A 662 LYS cc_start: 0.8626 (mttt) cc_final: 0.8254 (mtmt) REVERT: B 150 LEU cc_start: 0.8469 (mp) cc_final: 0.8258 (mp) outliers start: 24 outliers final: 16 residues processed: 191 average time/residue: 0.1222 time to fit residues: 28.9660 Evaluate side-chains 196 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103746 restraints weight = 10667.604| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.08 r_work: 0.3176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7281 Z= 0.181 Angle : 0.613 9.992 9843 Z= 0.305 Chirality : 0.042 0.144 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.402 18.308 977 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.80 % Allowed : 17.28 % Favored : 79.92 % 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 aren not related in a simple way. whole: -0.02 (0.28), residues: 903 helix: 1.33 (0.30), residues: 319 sheet: -0.40 (0.41), residues: 153 loop : -0.87 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.018 0.001 TYR A 633 PHE 0.017 0.001 PHE A 127 TRP 0.013 0.001 TRP B 14 HIS 0.003 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7271) covalent geometry : angle 0.59878 ( 9837) hydrogen bonds : bond 0.04391 ( 288) hydrogen bonds : angle 4.43076 ( 822) metal coordination : bond 0.00438 ( 10) metal coordination : angle 5.30890 ( 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: 22 poor density : 184 time to evaluate : 0.314 Fit side-chains REVERT: A 23 ARG cc_start: 0.8026 (mpt-90) cc_final: 0.7733 (mpt-90) REVERT: A 145 LYS cc_start: 0.8632 (tttt) cc_final: 0.8387 (tttp) REVERT: A 331 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: A 376 ASN cc_start: 0.7877 (t0) cc_final: 0.7601 (t0) REVERT: A 433 PHE cc_start: 0.8587 (m-80) cc_final: 0.8292 (m-80) REVERT: A 659 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7869 (mtpp) REVERT: A 662 LYS cc_start: 0.8629 (mttt) cc_final: 0.8248 (mtmt) REVERT: B 160 LYS cc_start: 0.8555 (mptt) cc_final: 0.8246 (mptt) outliers start: 22 outliers final: 19 residues processed: 190 average time/residue: 0.1246 time to fit residues: 29.6777 Evaluate side-chains 200 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 439 LEU 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 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 overall best weight: 0.4530 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.118749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104167 restraints weight = 10607.746| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.08 r_work: 0.3180 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1760 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= 0.149 Angle : 0.601 10.112 9843 Z= 0.300 Chirality : 0.041 0.139 1083 Planarity : 0.004 0.040 1276 Dihedral : 4.370 18.407 977 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.43 % Allowed : 17.03 % Favored : 79.54 % 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 aren not related in a simple way. whole: 0.00 (0.28), residues: 903 helix: 1.36 (0.29), residues: 318 sheet: -0.26 (0.43), residues: 146 loop : -0.91 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.015 0.001 TYR A 633 PHE 0.017 0.001 PHE A 127 TRP 0.012 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7271) covalent geometry : angle 0.58790 ( 9837) hydrogen bonds : bond 0.04265 ( 288) hydrogen bonds : angle 4.39735 ( 822) metal coordination : bond 0.00353 ( 10) metal coordination : angle 5.00247 ( 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 : 0.289 Fit side-chains REVERT: A 6 MET cc_start: 0.8030 (mtt) cc_final: 0.7701 (mtt) REVERT: A 23 ARG cc_start: 0.8004 (mpt-90) cc_final: 0.7704 (mpt-90) REVERT: A 145 LYS cc_start: 0.8634 (tttt) cc_final: 0.8386 (tttm) REVERT: A 322 MET cc_start: 0.8416 (tpp) cc_final: 0.8169 (tpt) REVERT: A 331 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 376 ASN cc_start: 0.7860 (t0) cc_final: 0.7582 (t0) REVERT: A 377 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7980 (mmm-85) REVERT: A 500 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 552 ASP cc_start: 0.7469 (t0) cc_final: 0.7246 (t70) REVERT: A 659 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8054 (mtmm) REVERT: A 662 LYS cc_start: 0.8643 (mttt) cc_final: 0.8231 (mtmt) REVERT: B 160 LYS cc_start: 0.8545 (mptt) cc_final: 0.8230 (mptt) outliers start: 27 outliers final: 18 residues processed: 192 average time/residue: 0.1180 time to fit residues: 28.1881 Evaluate side-chains 197 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 382 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 ILE 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 50 LYS Chi-restraints excluded: chain B residue 70 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: 0.6980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.0010 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.118601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103971 restraints weight = 10743.420| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.11 r_work: 0.3180 rms_B_bonded: 2.51 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: 0.7900 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7281 Z= 0.162 Angle : 0.610 10.150 9843 Z= 0.305 Chirality : 0.042 0.142 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.373 18.109 977 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.80 % Allowed : 18.42 % Favored : 78.78 % 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 aren not related in a simple way. whole: -0.03 (0.28), residues: 903 helix: 1.30 (0.30), residues: 319 sheet: -0.42 (0.42), residues: 153 loop : -0.85 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.014 0.001 TYR A 633 PHE 0.017 0.001 PHE A 127 TRP 0.013 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7271) covalent geometry : angle 0.59688 ( 9837) hydrogen bonds : bond 0.04316 ( 288) hydrogen bonds : angle 4.40693 ( 822) metal coordination : bond 0.00374 ( 10) metal coordination : angle 5.11192 ( 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 204 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.228 Fit side-chains REVERT: A 6 MET cc_start: 0.8059 (mtt) cc_final: 0.7747 (mtt) REVERT: A 23 ARG cc_start: 0.8004 (mpt-90) cc_final: 0.7695 (mpt-90) REVERT: A 145 LYS cc_start: 0.8640 (tttt) cc_final: 0.8398 (tttm) REVERT: A 322 MET cc_start: 0.8411 (tpp) cc_final: 0.8146 (tpt) REVERT: A 331 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: A 376 ASN cc_start: 0.7866 (t0) cc_final: 0.7601 (t0) REVERT: A 377 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7984 (mmm-85) REVERT: A 500 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7827 (mt) REVERT: A 552 ASP cc_start: 0.7643 (t0) cc_final: 0.7424 (t70) REVERT: A 659 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8041 (mtmm) REVERT: A 662 LYS cc_start: 0.8598 (mttt) cc_final: 0.8040 (mtmt) REVERT: A 663 GLU cc_start: 0.8495 (mp0) cc_final: 0.7947 (mp0) REVERT: B 160 LYS cc_start: 0.8574 (mptt) cc_final: 0.8254 (mptt) outliers start: 22 outliers final: 19 residues processed: 189 average time/residue: 0.1248 time to fit residues: 29.2175 Evaluate side-chains 200 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 382 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 ILE 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 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: 0.7980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.117978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103352 restraints weight = 10705.898| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.09 r_work: 0.3171 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7281 Z= 0.184 Angle : 0.625 10.307 9843 Z= 0.313 Chirality : 0.042 0.147 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.428 17.991 977 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.05 % Allowed : 18.30 % Favored : 78.65 % 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 aren not related in a simple way. whole: -0.08 (0.28), residues: 903 helix: 1.24 (0.29), residues: 319 sheet: -0.42 (0.40), residues: 159 loop : -0.88 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.015 0.001 TYR A 633 PHE 0.019 0.001 PHE A 127 TRP 0.014 0.001 TRP B 14 HIS 0.003 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7271) covalent geometry : angle 0.61145 ( 9837) hydrogen bonds : bond 0.04446 ( 288) hydrogen bonds : angle 4.48824 ( 822) metal coordination : bond 0.00405 ( 10) metal coordination : angle 5.24786 ( 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 205 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.348 Fit side-chains REVERT: A 6 MET cc_start: 0.8107 (mtt) cc_final: 0.7803 (mtt) REVERT: A 145 LYS cc_start: 0.8656 (tttt) cc_final: 0.8415 (tttm) REVERT: A 322 MET cc_start: 0.8421 (tpp) cc_final: 0.8158 (tpt) REVERT: A 331 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: A 376 ASN cc_start: 0.7886 (t0) cc_final: 0.7623 (t0) REVERT: A 377 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7950 (mmm-85) REVERT: A 500 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 659 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8064 (mtmm) REVERT: A 662 LYS cc_start: 0.8585 (mttt) cc_final: 0.8029 (mtmt) REVERT: A 663 GLU cc_start: 0.8474 (mp0) cc_final: 0.7936 (mp0) REVERT: B 160 LYS cc_start: 0.8566 (mptt) cc_final: 0.8251 (mptt) outliers start: 24 outliers final: 20 residues processed: 188 average time/residue: 0.1185 time to fit residues: 27.8587 Evaluate side-chains 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 ILE 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 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.0060 chunk 21 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.119637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104900 restraints weight = 10555.055| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.10 r_work: 0.3203 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 0.046 7281 Z= 0.118 Angle : 0.592 10.151 9843 Z= 0.297 Chirality : 0.041 0.149 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.323 17.583 977 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.03 % Allowed : 20.08 % 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 aren not related in a simple way. whole: 0.08 (0.29), residues: 903 helix: 1.37 (0.30), residues: 317 sheet: -0.25 (0.44), residues: 146 loop : -0.79 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.013 0.001 TYR A 633 PHE 0.014 0.001 PHE A 476 TRP 0.011 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7271) covalent geometry : angle 0.58183 ( 9837) hydrogen bonds : bond 0.04013 ( 288) hydrogen bonds : angle 4.36579 ( 822) metal coordination : bond 0.00297 ( 10) metal coordination : angle 4.57080 ( 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 196 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.306 Fit side-chains REVERT: A 6 MET cc_start: 0.8044 (mtt) cc_final: 0.7728 (mtt) REVERT: A 145 LYS cc_start: 0.8605 (tttt) cc_final: 0.8335 (tttp) REVERT: A 322 MET cc_start: 0.8374 (tpp) cc_final: 0.8137 (tpt) REVERT: A 376 ASN cc_start: 0.7810 (t0) cc_final: 0.7540 (t0) REVERT: A 500 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 552 ASP cc_start: 0.7613 (t0) cc_final: 0.7383 (t70) REVERT: A 659 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8018 (mtmm) REVERT: A 662 LYS cc_start: 0.8577 (mttt) cc_final: 0.8029 (mtmt) REVERT: A 663 GLU cc_start: 0.8462 (mp0) cc_final: 0.7945 (mp0) REVERT: B 160 LYS cc_start: 0.8531 (mptt) cc_final: 0.8215 (mptt) outliers start: 16 outliers final: 13 residues processed: 185 average time/residue: 0.1289 time to fit residues: 29.5600 Evaluate side-chains 190 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 ILE 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 Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.0040 chunk 29 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.118831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104099 restraints weight = 10648.800| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.11 r_work: 0.3191 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1963 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= 0.141 Angle : 0.607 10.179 9843 Z= 0.304 Chirality : 0.041 0.140 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.306 19.440 977 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.29 % Allowed : 19.95 % Favored : 77.76 % 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 aren not related in a simple way. whole: 0.04 (0.29), residues: 903 helix: 1.32 (0.30), residues: 318 sheet: -0.20 (0.43), residues: 152 loop : -0.84 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.015 0.001 TYR A 633 PHE 0.017 0.001 PHE A 127 TRP 0.014 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7271) covalent geometry : angle 0.59492 ( 9837) hydrogen bonds : bond 0.04138 ( 288) hydrogen bonds : angle 4.35881 ( 822) metal coordination : bond 0.00324 ( 10) metal coordination : angle 4.85200 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.45 seconds wall clock time: 37 minutes 17.16 seconds (2237.16 seconds total)