Starting phenix.real_space_refine on Wed Mar 12 03:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cah_45391/03_2025/9cah_45391_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cah_45391/03_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_45391/03_2025/9cah_45391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cah_45391/03_2025/9cah_45391.map" model { file = "/net/cci-nas-00/data/ceres_data/9cah_45391/03_2025/9cah_45391_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cah_45391/03_2025/9cah_45391_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.21, per 1000 atoms: 0.73 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.83 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: 1.95 Time building geometry restraints manager: 2.03 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: 3.340 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.070 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- 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 : 0.003 0.037 7271 Z= 0.192 Angle : 0.613 7.238 9837 Z= 0.340 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP B 161 HIS 0.003 0.000 HIS B 156 PHE 0.010 0.001 PHE A 235 TYR 0.014 0.001 TYR A 411 ARG 0.004 0.000 ARG A 665 *********************** 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 : 0.778 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: 0.2533 time to fit residues: 61.7771 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 : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 97 ASN A 218 GLN A 382 HIS A 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106525 restraints weight = 10533.221| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3214 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7271 Z= 0.267 Angle : 0.622 9.577 9837 Z= 0.313 Chirality : 0.042 0.150 1083 Planarity : 0.004 0.060 1276 Dihedral : 4.381 18.800 977 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.65 % Allowed : 10.55 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 903 helix: 1.41 (0.30), residues: 311 sheet: -0.29 (0.45), residues: 142 loop : -0.86 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 14 HIS 0.004 0.001 HIS A 642 PHE 0.012 0.001 PHE A 596 TYR 0.013 0.001 TYR A 685 ARG 0.003 0.000 ARG A 524 *********************** 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 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.771 Fit side-chains REVERT: A 145 LYS cc_start: 0.8593 (tttt) cc_final: 0.8377 (tttm) REVERT: A 281 LYS cc_start: 0.8515 (ptpt) cc_final: 0.8298 (ptpp) REVERT: A 376 ASN cc_start: 0.7934 (t0) cc_final: 0.7628 (t0) REVERT: A 552 ASP cc_start: 0.7891 (t0) cc_final: 0.7675 (t0) REVERT: A 632 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8347 (mttm) REVERT: A 662 LYS cc_start: 0.8617 (mttt) cc_final: 0.8245 (mtmt) REVERT: A 665 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7748 (ttm-80) outliers start: 13 outliers final: 8 residues processed: 185 average time/residue: 0.2553 time to fit residues: 58.8503 Evaluate side-chains 180 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 CYS 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 683 LYS 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 21 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 78 optimal weight: 0.1980 chunk 69 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.120986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106264 restraints weight = 10513.444| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.10 r_work: 0.3220 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7271 Z= 0.176 Angle : 0.577 8.842 9837 Z= 0.289 Chirality : 0.040 0.140 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.314 19.875 977 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.03 % Allowed : 13.34 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 903 helix: 1.46 (0.30), residues: 311 sheet: -0.32 (0.45), residues: 141 loop : -0.84 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 14 HIS 0.003 0.001 HIS A 711 PHE 0.008 0.001 PHE A 596 TYR 0.013 0.001 TYR A 411 ARG 0.003 0.000 ARG A 524 *********************** 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 194 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.873 Fit side-chains REVERT: A 145 LYS cc_start: 0.8587 (tttt) cc_final: 0.8346 (tttm) REVERT: A 281 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8300 (ptpp) REVERT: A 357 GLN cc_start: 0.8318 (mt0) cc_final: 0.7988 (mt0) REVERT: A 376 ASN cc_start: 0.7836 (t0) cc_final: 0.7539 (t0) REVERT: A 552 ASP cc_start: 0.7862 (t0) cc_final: 0.7653 (t0) REVERT: A 632 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8385 (mttm) REVERT: A 662 LYS cc_start: 0.8630 (mttt) cc_final: 0.8308 (mtmt) outliers start: 16 outliers final: 8 residues processed: 183 average time/residue: 0.2657 time to fit residues: 60.8815 Evaluate side-chains 185 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR 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 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 55 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.119856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105051 restraints weight = 10677.839| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3205 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7271 Z= 0.228 Angle : 0.586 9.365 9837 Z= 0.294 Chirality : 0.041 0.144 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.327 19.771 977 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.29 % Allowed : 14.74 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.29), residues: 903 helix: 1.42 (0.30), residues: 313 sheet: -0.38 (0.45), residues: 142 loop : -0.82 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 14 HIS 0.004 0.001 HIS A 628 PHE 0.011 0.001 PHE A 596 TYR 0.012 0.001 TYR A 411 ARG 0.004 0.000 ARG A 524 *********************** 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 200 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.850 Fit side-chains REVERT: A 23 ARG cc_start: 0.7998 (mpt-90) cc_final: 0.7696 (mpt-90) REVERT: A 93 ASN cc_start: 0.7748 (t0) cc_final: 0.7520 (t0) REVERT: A 145 LYS cc_start: 0.8633 (tttt) cc_final: 0.8397 (tttm) REVERT: A 281 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8334 (ptpp) REVERT: A 331 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: A 357 GLN cc_start: 0.8317 (mt0) cc_final: 0.8022 (mt0) REVERT: A 376 ASN cc_start: 0.7857 (t0) cc_final: 0.7578 (t0) REVERT: A 433 PHE cc_start: 0.8565 (m-80) cc_final: 0.8285 (m-80) REVERT: A 632 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8398 (mttm) REVERT: A 659 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7754 (mtpp) REVERT: A 662 LYS cc_start: 0.8632 (mttt) cc_final: 0.8274 (mtmt) outliers start: 18 outliers final: 13 residues processed: 188 average time/residue: 0.2723 time to fit residues: 63.4335 Evaluate side-chains 192 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR 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 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 7 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104679 restraints weight = 10569.940| |-----------------------------------------------------------------------------| r_work (start): 0.3323 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: 4.40 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7271 Z= 0.226 Angle : 0.581 9.562 9837 Z= 0.294 Chirality : 0.041 0.143 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.315 19.332 977 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.80 % Allowed : 15.63 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.29), residues: 903 helix: 1.42 (0.30), residues: 313 sheet: -0.41 (0.44), residues: 142 loop : -0.81 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 14 HIS 0.004 0.001 HIS A 628 PHE 0.011 0.001 PHE A 596 TYR 0.018 0.001 TYR A 633 ARG 0.004 0.000 ARG A 524 *********************** 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 206 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.871 Fit side-chains REVERT: A 23 ARG cc_start: 0.8011 (mpt-90) cc_final: 0.7690 (mpt-90) REVERT: A 93 ASN cc_start: 0.7773 (t0) cc_final: 0.7535 (t0) REVERT: A 145 LYS cc_start: 0.8623 (tttt) cc_final: 0.8378 (tttp) REVERT: A 186 LEU cc_start: 0.8332 (tp) cc_final: 0.8054 (tt) REVERT: A 281 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8331 (ptpp) REVERT: A 331 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 376 ASN cc_start: 0.7828 (t0) cc_final: 0.7560 (t0) REVERT: A 632 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8425 (mttm) REVERT: A 659 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7803 (mtpp) REVERT: A 662 LYS cc_start: 0.8642 (mttt) cc_final: 0.8297 (mtmt) outliers start: 22 outliers final: 15 residues processed: 190 average time/residue: 0.2771 time to fit residues: 65.1074 Evaluate side-chains 197 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 478 VAL 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 81 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103583 restraints weight = 10626.519| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.08 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7271 Z= 0.293 Angle : 0.610 10.005 9837 Z= 0.310 Chirality : 0.043 0.148 1083 Planarity : 0.004 0.040 1276 Dihedral : 4.414 20.046 977 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.43 % Allowed : 15.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 903 helix: 1.33 (0.29), residues: 320 sheet: -0.41 (0.42), residues: 153 loop : -0.87 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 14 HIS 0.004 0.001 HIS A 628 PHE 0.014 0.001 PHE A 596 TYR 0.017 0.001 TYR A 633 ARG 0.008 0.000 ARG A 665 *********************** 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 217 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.851 Fit side-chains REVERT: A 23 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7745 (mpt-90) REVERT: A 93 ASN cc_start: 0.7879 (t0) cc_final: 0.7640 (t0) REVERT: A 145 LYS cc_start: 0.8642 (tttt) cc_final: 0.8400 (tttp) REVERT: A 331 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: A 376 ASN cc_start: 0.7887 (t0) cc_final: 0.7611 (t0) REVERT: A 632 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8398 (mttp) REVERT: A 659 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7857 (mtpp) REVERT: A 662 LYS cc_start: 0.8617 (mttt) cc_final: 0.8232 (mtmt) REVERT: B 160 LYS cc_start: 0.8565 (mptt) cc_final: 0.8260 (mptt) outliers start: 27 outliers final: 20 residues processed: 196 average time/residue: 0.2619 time to fit residues: 64.0495 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 : 0.788 ------------------------------------------------------------------------------- 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 51 ARG 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 356 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 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 104 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.3172 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.119155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104531 restraints weight = 10597.224| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.10 r_work: 0.3194 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7271 Z= 0.187 Angle : 0.573 9.688 9837 Z= 0.292 Chirality : 0.040 0.141 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.333 20.062 977 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.05 % Allowed : 16.77 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 903 helix: 1.41 (0.30), residues: 319 sheet: -0.29 (0.43), residues: 146 loop : -0.87 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 14 HIS 0.002 0.001 HIS A 29 PHE 0.010 0.001 PHE A 235 TYR 0.015 0.001 TYR A 633 ARG 0.006 0.000 ARG A 377 *********************** 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 210 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.925 Fit side-chains REVERT: A 93 ASN cc_start: 0.7809 (t0) cc_final: 0.7598 (t0) REVERT: A 145 LYS cc_start: 0.8621 (tttt) cc_final: 0.8369 (tttp) REVERT: A 267 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7772 (ttm-80) REVERT: A 331 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: A 376 ASN cc_start: 0.7846 (t0) cc_final: 0.7586 (t0) REVERT: A 377 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: A 433 PHE cc_start: 0.8579 (m-80) cc_final: 0.8317 (m-80) REVERT: A 632 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8379 (mttp) REVERT: A 659 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7819 (mtpp) REVERT: A 662 LYS cc_start: 0.8635 (mttt) cc_final: 0.8207 (mtmt) REVERT: B 160 LYS cc_start: 0.8543 (mptt) cc_final: 0.8234 (mptt) outliers start: 24 outliers final: 15 residues processed: 195 average time/residue: 0.2764 time to fit residues: 67.3394 Evaluate side-chains 199 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.116953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102421 restraints weight = 10677.987| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.08 r_work: 0.3154 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7271 Z= 0.368 Angle : 0.643 10.394 9837 Z= 0.327 Chirality : 0.044 0.153 1083 Planarity : 0.004 0.043 1276 Dihedral : 4.522 19.659 977 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.18 % Allowed : 17.66 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 903 helix: 1.22 (0.29), residues: 320 sheet: -0.54 (0.41), residues: 156 loop : -0.94 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 14 HIS 0.003 0.001 HIS A 29 PHE 0.017 0.002 PHE A 596 TYR 0.021 0.002 TYR A 633 ARG 0.008 0.000 ARG A 524 *********************** 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 207 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.874 Fit side-chains REVERT: A 6 MET cc_start: 0.8145 (mtt) cc_final: 0.7849 (mtt) REVERT: A 93 ASN cc_start: 0.7938 (t0) cc_final: 0.7648 (t0) REVERT: A 96 LEU cc_start: 0.8430 (mt) cc_final: 0.8049 (mt) REVERT: A 145 LYS cc_start: 0.8664 (tttt) cc_final: 0.8413 (tttp) REVERT: A 322 MET cc_start: 0.8406 (mmm) cc_final: 0.8128 (tpt) REVERT: A 331 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: A 376 ASN cc_start: 0.7968 (t0) cc_final: 0.7668 (t0) REVERT: A 433 PHE cc_start: 0.8597 (m-80) cc_final: 0.8346 (m-80) REVERT: A 520 ASN cc_start: 0.7902 (t0) cc_final: 0.7485 (m110) REVERT: A 659 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7933 (mtpp) REVERT: A 662 LYS cc_start: 0.8634 (mttt) cc_final: 0.8096 (mtmt) REVERT: A 663 GLU cc_start: 0.8458 (mp0) cc_final: 0.7909 (mp0) REVERT: B 160 LYS cc_start: 0.8616 (mptt) cc_final: 0.8306 (mptt) outliers start: 25 outliers final: 21 residues processed: 188 average time/residue: 0.2724 time to fit residues: 64.0246 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 : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 51 ARG 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 382 HIS 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 B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103537 restraints weight = 10732.486| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.09 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7271 Z= 0.279 Angle : 0.621 10.389 9837 Z= 0.316 Chirality : 0.043 0.151 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.519 19.887 977 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.67 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 903 helix: 1.20 (0.29), residues: 320 sheet: -0.47 (0.42), residues: 153 loop : -0.92 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 14 HIS 0.003 0.001 HIS A 642 PHE 0.013 0.001 PHE A 235 TYR 0.020 0.001 TYR A 633 ARG 0.006 0.000 ARG A 524 *********************** 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: 21 poor density : 182 time to evaluate : 0.778 Fit side-chains REVERT: A 6 MET cc_start: 0.8117 (mtt) cc_final: 0.7826 (mtt) REVERT: A 93 ASN cc_start: 0.7926 (t0) cc_final: 0.7644 (t0) REVERT: A 96 LEU cc_start: 0.8429 (mt) cc_final: 0.8053 (mt) REVERT: A 145 LYS cc_start: 0.8637 (tttt) cc_final: 0.8397 (tttp) REVERT: A 322 MET cc_start: 0.8408 (mmm) cc_final: 0.8157 (tpt) REVERT: A 331 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: A 376 ASN cc_start: 0.7890 (t0) cc_final: 0.7617 (t0) REVERT: A 377 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: A 433 PHE cc_start: 0.8586 (m-80) cc_final: 0.8333 (m-80) REVERT: A 632 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8404 (mtmm) REVERT: A 659 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7887 (mtpp) REVERT: A 662 LYS cc_start: 0.8604 (mttt) cc_final: 0.8037 (mtmt) REVERT: A 663 GLU cc_start: 0.8466 (mp0) cc_final: 0.7937 (mp0) REVERT: B 160 LYS cc_start: 0.8577 (mptt) cc_final: 0.8278 (mptt) outliers start: 21 outliers final: 17 residues processed: 187 average time/residue: 0.2673 time to fit residues: 62.5276 Evaluate side-chains 198 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 51 ARG 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102773 restraints weight = 10910.121| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.10 r_work: 0.3159 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7271 Z= 0.324 Angle : 0.639 10.629 9837 Z= 0.326 Chirality : 0.044 0.172 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.563 19.981 977 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.67 % Allowed : 19.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 903 helix: 1.16 (0.29), residues: 320 sheet: -0.47 (0.42), residues: 153 loop : -0.95 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 PHE 0.014 0.001 PHE A 596 TYR 0.021 0.002 TYR A 633 ARG 0.007 0.000 ARG A 524 ********************** 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: 21 poor density : 175 time to evaluate : 0.804 Fit side-chains REVERT: A 6 MET cc_start: 0.8154 (mtt) cc_final: 0.7872 (mtt) REVERT: A 93 ASN cc_start: 0.7907 (t0) cc_final: 0.7626 (t0) REVERT: A 96 LEU cc_start: 0.8429 (mt) cc_final: 0.8054 (mt) REVERT: A 145 LYS cc_start: 0.8642 (tttt) cc_final: 0.8398 (tttp) REVERT: A 322 MET cc_start: 0.8399 (mmm) cc_final: 0.8142 (tpt) REVERT: A 331 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: A 376 ASN cc_start: 0.7969 (t0) cc_final: 0.7679 (t0) REVERT: A 377 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: A 632 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8394 (mtmm) REVERT: A 659 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7902 (mtpp) REVERT: A 662 LYS cc_start: 0.8604 (mttt) cc_final: 0.8038 (mtmt) REVERT: A 663 GLU cc_start: 0.8468 (mp0) cc_final: 0.7942 (mp0) REVERT: B 160 LYS cc_start: 0.8611 (mptt) cc_final: 0.8309 (mptt) outliers start: 21 outliers final: 18 residues processed: 182 average time/residue: 0.2678 time to fit residues: 60.5358 Evaluate side-chains 194 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 51 ARG 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 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 483 MET 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 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 0.0670 chunk 81 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103963 restraints weight = 10641.834| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.10 r_work: 0.3188 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7271 Z= 0.208 Angle : 0.605 10.243 9837 Z= 0.308 Chirality : 0.041 0.148 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.442 19.924 977 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.41 % Allowed : 19.19 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 903 helix: 1.28 (0.30), residues: 319 sheet: -0.38 (0.42), residues: 152 loop : -0.93 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 458 HIS 0.002 0.001 HIS A 29 PHE 0.013 0.001 PHE A 476 TYR 0.017 0.001 TYR A 633 ARG 0.005 0.000 ARG A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.24 seconds wall clock time: 78 minutes 8.90 seconds (4688.90 seconds total)