Starting phenix.real_space_refine on Wed Feb 12 03:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cah_45391/02_2025/9cah_45391_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cah_45391/02_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_45391/02_2025/9cah_45391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cah_45391/02_2025/9cah_45391.map" model { file = "/net/cci-nas-00/data/ceres_data/9cah_45391/02_2025/9cah_45391_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cah_45391/02_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-5592/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: 5.19, 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: 1.67 Conformation dependent library (CDL) restraints added in 1.0 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: 0.76 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: 2.01 Time building geometry restraints manager: 1.97 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: 2.440 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- 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 : 0.734 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: 0.2535 time to fit residues: 62.0337 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 : 0.827 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106529 restraints weight = 10533.226| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3215 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 9.578 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 : 0.723 Fit side-chains REVERT: A 145 LYS cc_start: 0.8593 (tttt) cc_final: 0.8377 (tttm) REVERT: A 281 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8296 (ptpp) REVERT: A 376 ASN cc_start: 0.7936 (t0) cc_final: 0.7629 (t0) REVERT: A 552 ASP cc_start: 0.7890 (t0) cc_final: 0.7676 (t0) REVERT: A 632 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8346 (mttm) REVERT: A 662 LYS cc_start: 0.8615 (mttt) cc_final: 0.8243 (mtmt) REVERT: A 665 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7749 (ttm-80) outliers start: 13 outliers final: 8 residues processed: 185 average time/residue: 0.2646 time to fit residues: 60.9164 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 : 0.794 ------------------------------------------------------------------------------- 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: 0.5980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.0670 chunk 69 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.121059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106334 restraints weight = 10520.190| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.10 r_work: 0.3229 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1233 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= 0.174 Angle : 0.575 8.759 9837 Z= 0.288 Chirality : 0.040 0.139 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.311 19.910 977 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.03 % Allowed : 13.21 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (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 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.713 Fit side-chains REVERT: A 145 LYS cc_start: 0.8582 (tttt) cc_final: 0.8341 (tttm) REVERT: A 185 ASP cc_start: 0.7516 (m-30) cc_final: 0.7312 (m-30) REVERT: A 281 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8305 (ptpp) REVERT: A 357 GLN cc_start: 0.8317 (mt0) cc_final: 0.8042 (mt0) REVERT: A 376 ASN cc_start: 0.7830 (t0) cc_final: 0.7537 (t0) REVERT: A 552 ASP cc_start: 0.7856 (t0) cc_final: 0.7656 (t0) REVERT: A 632 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8391 (mttm) REVERT: A 662 LYS cc_start: 0.8629 (mttt) cc_final: 0.8304 (mtmt) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.2575 time to fit residues: 59.1267 Evaluate side-chains 186 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.119753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104891 restraints weight = 10660.170| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.13 r_work: 0.3205 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7271 Z= 0.232 Angle : 0.588 9.354 9837 Z= 0.295 Chirality : 0.041 0.145 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.320 17.731 977 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.41 % Allowed : 14.99 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.29), residues: 903 helix: 1.45 (0.30), residues: 311 sheet: -0.38 (0.45), residues: 142 loop : -0.79 (0.30), residues: 450 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 201 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.809 Fit side-chains REVERT: A 93 ASN cc_start: 0.7751 (t0) cc_final: 0.7527 (t0) REVERT: A 145 LYS cc_start: 0.8630 (tttt) cc_final: 0.8395 (tttm) REVERT: A 185 ASP cc_start: 0.7581 (m-30) cc_final: 0.7347 (m-30) REVERT: A 281 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8333 (ptpp) REVERT: A 331 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: A 357 GLN cc_start: 0.8311 (mt0) cc_final: 0.8021 (mt0) REVERT: A 376 ASN cc_start: 0.7855 (t0) cc_final: 0.7574 (t0) REVERT: A 433 PHE cc_start: 0.8564 (m-80) cc_final: 0.8290 (m-80) REVERT: A 632 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8402 (mttm) REVERT: A 659 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7789 (mtpp) REVERT: A 662 LYS cc_start: 0.8631 (mttt) cc_final: 0.8282 (mtmt) outliers start: 19 outliers final: 13 residues processed: 188 average time/residue: 0.2746 time to fit residues: 64.3689 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 : 0.809 ------------------------------------------------------------------------------- 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: 0.0770 chunk 16 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104719 restraints weight = 10562.515| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.11 r_work: 0.3205 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7271 Z= 0.224 Angle : 0.583 9.492 9837 Z= 0.293 Chirality : 0.041 0.142 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.301 18.248 977 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.54 % Allowed : 16.14 % 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 (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: 1.42 (0.30), residues: 313 sheet: -0.41 (0.44), residues: 142 loop : -0.79 (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 202 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.851 Fit side-chains REVERT: A 23 ARG cc_start: 0.8014 (mpt-90) cc_final: 0.7694 (mpt-90) REVERT: A 93 ASN cc_start: 0.7771 (t0) cc_final: 0.7535 (t0) REVERT: A 145 LYS cc_start: 0.8627 (tttt) cc_final: 0.8385 (tttp) REVERT: A 185 ASP cc_start: 0.7574 (m-30) cc_final: 0.7304 (m-30) REVERT: A 281 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8335 (ptpp) REVERT: A 331 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: A 376 ASN cc_start: 0.7833 (t0) cc_final: 0.7561 (t0) REVERT: A 632 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8419 (mttm) REVERT: A 659 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7814 (mtpp) REVERT: A 662 LYS cc_start: 0.8634 (mttt) cc_final: 0.8295 (mtmt) outliers start: 20 outliers final: 14 residues processed: 186 average time/residue: 0.2712 time to fit residues: 62.5566 Evaluate side-chains 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 8 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.119222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104457 restraints weight = 10604.875| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.11 r_work: 0.3192 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7271 Z= 0.223 Angle : 0.580 9.612 9837 Z= 0.292 Chirality : 0.041 0.141 1083 Planarity : 0.004 0.040 1276 Dihedral : 4.288 18.291 977 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: 0.07 (0.29), residues: 903 helix: 1.43 (0.30), residues: 313 sheet: -0.41 (0.44), residues: 142 loop : -0.78 (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 0.016 0.001 TYR A 633 ARG 0.007 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 209 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.842 Fit side-chains REVERT: A 23 ARG cc_start: 0.8026 (mpt-90) cc_final: 0.7743 (mpt-90) REVERT: A 93 ASN cc_start: 0.7803 (t0) cc_final: 0.7576 (t0) REVERT: A 145 LYS cc_start: 0.8574 (tttt) cc_final: 0.8338 (tttp) REVERT: A 185 ASP cc_start: 0.7618 (m-30) cc_final: 0.7344 (m-30) REVERT: A 281 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8338 (ptpp) REVERT: A 331 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: A 376 ASN cc_start: 0.7844 (t0) cc_final: 0.7577 (t0) REVERT: A 433 PHE cc_start: 0.8574 (m-80) cc_final: 0.8299 (m-80) REVERT: A 632 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8427 (mttm) REVERT: A 659 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7829 (mtpp) REVERT: A 662 LYS cc_start: 0.8628 (mttt) cc_final: 0.8252 (mtmt) REVERT: B 150 LEU cc_start: 0.8472 (mp) cc_final: 0.8265 (mp) REVERT: B 160 LYS cc_start: 0.8521 (mptt) cc_final: 0.8203 (mptt) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 0.2850 time to fit residues: 68.2409 Evaluate side-chains 200 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 478 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 70 VAL 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: 0.1980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 88 optimal weight: 0.0010 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.2986 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.120004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105249 restraints weight = 10556.561| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3215 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7271 Z= 0.181 Angle : 0.563 9.771 9837 Z= 0.285 Chirality : 0.040 0.136 1083 Planarity : 0.004 0.040 1276 Dihedral : 4.237 18.070 977 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.92 % Allowed : 16.90 % 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: 0.16 (0.29), residues: 903 helix: 1.47 (0.30), residues: 318 sheet: -0.23 (0.46), residues: 135 loop : -0.77 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 14 HIS 0.002 0.001 HIS A 711 PHE 0.009 0.001 PHE A 596 TYR 0.014 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 208 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.770 Fit side-chains REVERT: A 93 ASN cc_start: 0.7769 (t0) cc_final: 0.7569 (t0) REVERT: A 145 LYS cc_start: 0.8573 (tttt) cc_final: 0.8314 (tttp) REVERT: A 185 ASP cc_start: 0.7624 (m-30) cc_final: 0.7338 (m-30) REVERT: A 267 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7762 (ttm-80) REVERT: A 281 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8328 (ptpp) REVERT: A 376 ASN cc_start: 0.7816 (t0) cc_final: 0.7531 (t0) REVERT: A 377 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: A 433 PHE cc_start: 0.8569 (m-80) cc_final: 0.8307 (m-80) REVERT: A 659 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7967 (mtmm) REVERT: A 662 LYS cc_start: 0.8636 (mttt) cc_final: 0.8212 (mtmt) REVERT: B 160 LYS cc_start: 0.8511 (mptt) cc_final: 0.8195 (mptt) outliers start: 23 outliers final: 15 residues processed: 192 average time/residue: 0.2753 time to fit residues: 65.2921 Evaluate side-chains 197 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 368 LYS Chi-restraints excluded: chain A residue 478 VAL 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 185 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: 0.3980 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 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 271 GLN 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 = 0.118016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103364 restraints weight = 10652.076| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.09 r_work: 0.3172 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7271 Z= 0.320 Angle : 0.625 10.128 9837 Z= 0.316 Chirality : 0.043 0.151 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.411 17.905 977 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.41 % Allowed : 17.92 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.29), residues: 903 helix: 1.31 (0.29), residues: 320 sheet: -0.39 (0.42), residues: 153 loop : -0.82 (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 0.015 0.002 PHE A 596 TYR 0.019 0.002 TYR A 633 ARG 0.006 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 205 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.905 Fit side-chains REVERT: A 6 MET cc_start: 0.8089 (mtt) cc_final: 0.7780 (mtt) REVERT: A 23 ARG cc_start: 0.8062 (mpt-90) cc_final: 0.7855 (mpp80) REVERT: A 93 ASN cc_start: 0.7892 (t0) cc_final: 0.7669 (t0) REVERT: A 145 LYS cc_start: 0.8620 (tttt) cc_final: 0.8353 (tttp) REVERT: A 185 ASP cc_start: 0.7633 (m-30) cc_final: 0.7350 (m-30) REVERT: A 322 MET cc_start: 0.8479 (tpp) cc_final: 0.8279 (tpt) REVERT: A 376 ASN cc_start: 0.7973 (t0) cc_final: 0.7663 (t0) REVERT: A 433 PHE cc_start: 0.8566 (m-80) cc_final: 0.8288 (m-80) REVERT: A 552 ASP cc_start: 0.7509 (t0) cc_final: 0.7300 (t70) REVERT: A 659 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7859 (mtpp) REVERT: A 662 LYS cc_start: 0.8623 (mttt) cc_final: 0.8083 (mtmt) REVERT: A 663 GLU cc_start: 0.8467 (mp0) cc_final: 0.7944 (mp0) REVERT: B 160 LYS cc_start: 0.8581 (mptt) cc_final: 0.8267 (mptt) outliers start: 19 outliers final: 17 residues processed: 191 average time/residue: 0.2667 time to fit residues: 63.9575 Evaluate side-chains 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 356 GLN Chi-restraints excluded: chain A residue 478 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 0.0010 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.118732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104128 restraints weight = 10709.930| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.09 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7271 Z= 0.259 Angle : 0.607 10.387 9837 Z= 0.307 Chirality : 0.042 0.166 1083 Planarity : 0.004 0.041 1276 Dihedral : 4.408 17.830 977 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % 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 (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: -0.02 (0.29), residues: 903 helix: 1.31 (0.29), residues: 319 sheet: -0.40 (0.41), residues: 159 loop : -0.86 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 PHE 0.012 0.001 PHE A 596 TYR 0.019 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 204 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.841 Fit side-chains REVERT: A 6 MET cc_start: 0.8050 (mtt) cc_final: 0.7731 (mtt) REVERT: A 23 ARG cc_start: 0.8032 (mpt-90) cc_final: 0.7820 (mpp80) REVERT: A 93 ASN cc_start: 0.7874 (t0) cc_final: 0.7662 (t0) REVERT: A 145 LYS cc_start: 0.8599 (tttt) cc_final: 0.8340 (tttp) REVERT: A 185 ASP cc_start: 0.7634 (m-30) cc_final: 0.7349 (m-30) REVERT: A 376 ASN cc_start: 0.7892 (t0) cc_final: 0.7620 (t0) REVERT: A 433 PHE cc_start: 0.8561 (m-80) cc_final: 0.8283 (m-80) REVERT: A 552 ASP cc_start: 0.7549 (t0) cc_final: 0.7327 (t70) REVERT: A 659 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8038 (mtmm) REVERT: A 662 LYS cc_start: 0.8594 (mttt) cc_final: 0.8033 (mtmt) REVERT: A 663 GLU cc_start: 0.8467 (mp0) cc_final: 0.7948 (mp0) REVERT: B 160 LYS cc_start: 0.8569 (mptt) cc_final: 0.8249 (mptt) outliers start: 16 outliers final: 14 residues processed: 191 average time/residue: 0.2659 time to fit residues: 63.1351 Evaluate side-chains 199 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 478 VAL 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 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.117805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103175 restraints weight = 10860.960| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7271 Z= 0.307 Angle : 0.626 10.446 9837 Z= 0.316 Chirality : 0.043 0.147 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.462 17.737 977 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.16 % Allowed : 19.44 % 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: -0.06 (0.29), residues: 903 helix: 1.25 (0.29), residues: 320 sheet: -0.40 (0.41), residues: 165 loop : -0.87 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 14 HIS 0.003 0.001 HIS A 642 PHE 0.014 0.002 PHE A 596 TYR 0.020 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 201 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.781 Fit side-chains REVERT: A 6 MET cc_start: 0.8110 (mtt) cc_final: 0.7834 (mtt) REVERT: A 23 ARG cc_start: 0.8052 (mpt-90) cc_final: 0.7819 (mpp80) REVERT: A 93 ASN cc_start: 0.7929 (t0) cc_final: 0.7653 (t0) REVERT: A 96 LEU cc_start: 0.8422 (mt) cc_final: 0.8039 (mt) REVERT: A 145 LYS cc_start: 0.8617 (tttt) cc_final: 0.8355 (tttp) REVERT: A 185 ASP cc_start: 0.7650 (m-30) cc_final: 0.7365 (m-30) REVERT: A 376 ASN cc_start: 0.7922 (t0) cc_final: 0.7617 (t0) REVERT: A 433 PHE cc_start: 0.8590 (m-80) cc_final: 0.8309 (m-80) REVERT: A 659 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8046 (mtmm) REVERT: A 662 LYS cc_start: 0.8591 (mttt) cc_final: 0.8026 (mtmt) REVERT: A 663 GLU cc_start: 0.8467 (mp0) cc_final: 0.7947 (mp0) REVERT: B 160 LYS cc_start: 0.8585 (mptt) cc_final: 0.8262 (mptt) outliers start: 17 outliers final: 16 residues processed: 187 average time/residue: 0.2750 time to fit residues: 63.4567 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 : 0.821 ------------------------------------------------------------------------------- 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 382 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 670 ASP 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 185 VAL 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: 0.9990 chunk 14 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.4860 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.118703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104146 restraints weight = 10644.189| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.08 r_work: 0.3190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1981 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= 0.245 Angle : 0.608 10.470 9837 Z= 0.307 Chirality : 0.042 0.145 1083 Planarity : 0.004 0.042 1276 Dihedral : 4.461 17.576 977 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.29 % Allowed : 19.31 % 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: -0.01 (0.29), residues: 903 helix: 1.29 (0.30), residues: 319 sheet: -0.34 (0.42), residues: 152 loop : -0.84 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 14 HIS 0.003 0.001 HIS A 29 PHE 0.011 0.001 PHE A 235 TYR 0.019 0.001 TYR A 633 ARG 0.006 0.000 ARG A 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.02 seconds wall clock time: 73 minutes 46.07 seconds (4426.07 seconds total)