Starting phenix.real_space_refine on Mon Jul 28 16:14:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.map" model { file = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2025/8iby_35349.cif" } resolution = 3.47 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= 0.010 sd= 0.085 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 Zn 1 6.06 5 P 198 5.49 5 S 32 5.16 5 C 5817 2.51 5 N 1973 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10503 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4233 Classifications: {'RNA': 198} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 91, 'rna3p_pyr': 75} Link IDs: {'rna2p': 32, 'rna3p': 165} Chain breaks: 3 Chain: "C" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6269 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 39, 'TRANS': 753} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9132 SG CYS C 934 59.637 71.301 25.232 1.00104.66 S ATOM 9158 SG CYS C 938 58.180 73.110 22.172 1.00109.37 S ATOM 9263 SG CYS C 951 55.829 71.305 24.654 1.00 93.60 S Time building chain proxies: 12.16, per 1000 atoms: 1.16 Number of scatterers: 10503 At special positions: 0 Unit cell: (107.594, 130.65, 119.671, 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 1 29.99 S 32 16.00 P 198 15.00 O 2482 8.00 N 1973 7.00 C 5817 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: 3.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 934 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 951 " Number of angles added : 3 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 54.6% alpha, 10.5% beta 57 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 8.84 Creating SS restraints... Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.553A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.928A pdb=" N LYS C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.937A pdb=" N VAL C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.577A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 519 Processing helix chain 'C' and resid 539 through 549 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 607 removed outlier: 3.628A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.624A pdb=" N MET C 640 " --> pdb=" O SER C 636 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 641 " --> pdb=" O LYS C 637 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 642 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.564A pdb=" N GLN C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 755 removed outlier: 3.884A pdb=" N LEU C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 removed outlier: 3.802A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 791 removed outlier: 4.177A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 816 removed outlier: 3.740A pdb=" N ILE C 807 " --> pdb=" O VAL C 803 " (cutoff:3.500A) Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 817 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.508A pdb=" N ARG C 827 " --> pdb=" O TRP C 823 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 849 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 875 through 879 Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.590A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.679A pdb=" N VAL C 904 " --> pdb=" O GLY C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.821A pdb=" N ARG C 922 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.736A pdb=" N LYS C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 Processing helix chain 'C' and resid 1066 through 1077 removed outlier: 3.710A pdb=" N ILE C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1105 removed outlier: 3.819A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) Proline residue: C1088 - end of helix removed outlier: 4.317A pdb=" N MET C1105 " --> pdb=" O ARG C1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467 Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 537 through 538 removed outlier: 4.429A pdb=" N VAL C 537 " --> pdb=" O GLY C 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA8, first strand: chain 'C' and resid 979 through 982 removed outlier: 3.762A pdb=" N THR C 979 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1000 " --> pdb=" O THR C 979 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1064 " --> pdb=" O SER C1060 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 11.47 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2787 1.34 - 1.46: 3602 1.46 - 1.58: 4301 1.58 - 1.70: 394 1.70 - 1.83: 46 Bond restraints: 11130 Sorted by residual: bond pdb=" CB PRO C 366 " pdb=" CG PRO C 366 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" CB PRO C 915 " pdb=" CG PRO C 915 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.27e+00 bond pdb=" CG1 ILE C 959 " pdb=" CD1 ILE C 959 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CB GLU C 974 " pdb=" CG GLU C 974 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C PRO C 364 " pdb=" N THR C 365 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.71e-02 3.42e+03 1.40e+00 ... (remaining 11125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15828 2.39 - 4.79: 155 4.79 - 7.18: 24 7.18 - 9.57: 2 9.57 - 11.96: 5 Bond angle restraints: 16014 Sorted by residual: angle pdb=" CA PRO C 366 " pdb=" N PRO C 366 " pdb=" CD PRO C 366 " ideal model delta sigma weight residual 112.00 104.01 7.99 1.40e+00 5.10e-01 3.26e+01 angle pdb=" CB MET C 428 " pdb=" CG MET C 428 " pdb=" SD MET C 428 " ideal model delta sigma weight residual 112.70 124.66 -11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C3' C E 267 " pdb=" O3' C E 267 " pdb=" P C E 268 " ideal model delta sigma weight residual 120.20 125.96 -5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C SER C 469 " pdb=" N ILE C 470 " pdb=" CA ILE C 470 " ideal model delta sigma weight residual 120.33 123.31 -2.98 8.00e-01 1.56e+00 1.39e+01 angle pdb=" CA PRO C 915 " pdb=" N PRO C 915 " pdb=" CD PRO C 915 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 16009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6257 35.45 - 70.90: 663 70.90 - 106.35: 71 106.35 - 141.80: 6 141.80 - 177.25: 3 Dihedral angle restraints: 7000 sinusoidal: 4726 harmonic: 2274 Sorted by residual: dihedral pdb=" O4' C E 145 " pdb=" C1' C E 145 " pdb=" N1 C E 145 " pdb=" C2 C E 145 " ideal model delta sinusoidal sigma weight residual -128.00 49.25 -177.25 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' U E 101 " pdb=" C3' U E 101 " pdb=" O3' U E 101 " pdb=" P G E 102 " ideal model delta sinusoidal sigma weight residual -140.00 29.63 -169.63 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" O4' G E 110 " pdb=" C1' G E 110 " pdb=" N9 G E 110 " pdb=" C4 G E 110 " ideal model delta sinusoidal sigma weight residual -106.00 -163.81 57.81 1 1.70e+01 3.46e-03 1.55e+01 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1651 0.046 - 0.091: 225 0.091 - 0.137: 57 0.137 - 0.183: 6 0.183 - 0.229: 3 Chirality restraints: 1942 Sorted by residual: chirality pdb=" C1' A E 56 " pdb=" O4' A E 56 " pdb=" C2' A E 56 " pdb=" N9 A E 56 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" P C E 268 " pdb=" OP1 C E 268 " pdb=" OP2 C E 268 " pdb=" O5' C E 268 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' U E 114 " pdb=" C4' U E 114 " pdb=" O3' U E 114 " pdb=" C2' U E 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1939 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 365 " -0.056 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 366 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 366 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 366 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C E 78 " 0.031 2.00e-02 2.50e+03 1.97e-02 8.77e+00 pdb=" N1 C E 78 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C E 78 " 0.023 2.00e-02 2.50e+03 pdb=" O2 C E 78 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C E 78 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C E 78 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C E 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C E 78 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C E 78 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 914 " -0.047 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO C 915 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 915 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 915 " -0.038 5.00e-02 4.00e+02 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 909 2.73 - 3.27: 10255 3.27 - 3.81: 18936 3.81 - 4.36: 21763 4.36 - 4.90: 33231 Nonbonded interactions: 85094 Sorted by model distance: nonbonded pdb=" O2' G E 112 " pdb=" O4' A E 113 " model vdw 2.187 3.040 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.206 3.040 nonbonded pdb=" O2 U E 136 " pdb=" N2 G E 152 " model vdw 2.207 2.496 nonbonded pdb=" NZ LYS C 389 " pdb=" O PRO C 390 " model vdw 2.230 3.120 nonbonded pdb=" N2 G E 33 " pdb=" OP2 A E 36 " model vdw 2.233 3.120 ... (remaining 85089 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: 129.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 58.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.120 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:4.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 0.124 11134 Z= 0.140 Angle : 0.622 11.963 16017 Z= 0.319 Chirality : 0.035 0.229 1942 Planarity : 0.005 0.081 1316 Dihedral : 23.522 177.250 5532 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 25.52 % Favored : 74.48 % 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 (0.31), residues: 789 helix: 1.47 (0.28), residues: 371 sheet: -2.02 (0.62), residues: 63 loop : -1.11 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 388 HIS 0.010 0.001 HIS C 955 PHE 0.025 0.002 PHE C 555 TYR 0.015 0.001 TYR C 703 ARG 0.008 0.000 ARG C 316 Details of bonding type rmsd hydrogen bonds : bond 0.14845 ( 444) hydrogen bonds : angle 5.74314 ( 1133) metal coordination : bond 0.00546 ( 4) metal coordination : angle 0.50472 ( 3) covalent geometry : bond 0.00333 (11130) covalent geometry : angle 0.62208 (16014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6763 (ptpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3911 time to fit residues: 41.5691 Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 88 optimal weight: 7.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS C 659 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116034 restraints weight = 21744.491| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.70 r_work: 0.3466 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 11134 Z= 0.114 Angle : 0.566 10.151 16017 Z= 0.284 Chirality : 0.035 0.221 1942 Planarity : 0.005 0.043 1316 Dihedral : 24.205 177.668 3993 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 1.94 % Allowed : 22.24 % Favored : 75.82 % 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: 0.29 (0.31), residues: 789 helix: 1.56 (0.28), residues: 387 sheet: -1.69 (0.64), residues: 64 loop : -1.05 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 388 HIS 0.007 0.001 HIS C 955 PHE 0.009 0.001 PHE C 749 TYR 0.010 0.001 TYR C 563 ARG 0.005 0.000 ARG C 316 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 444) hydrogen bonds : angle 4.38454 ( 1133) metal coordination : bond 0.00456 ( 4) metal coordination : angle 1.01276 ( 3) covalent geometry : bond 0.00249 (11130) covalent geometry : angle 0.56606 (16014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7258 (mtmm) cc_final: 0.6900 (mtmm) REVERT: C 446 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7226 (ptp-110) REVERT: C 868 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (m90) REVERT: C 1105 MET cc_start: 0.8011 (ppp) cc_final: 0.7736 (ppp) outliers start: 13 outliers final: 3 residues processed: 94 average time/residue: 0.2936 time to fit residues: 37.3781 Evaluate side-chains 76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 868 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 28 optimal weight: 40.0000 chunk 26 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.172127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110071 restraints weight = 22210.996| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.99 r_work: 0.3322 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11134 Z= 0.256 Angle : 0.686 10.139 16017 Z= 0.345 Chirality : 0.039 0.225 1942 Planarity : 0.006 0.046 1316 Dihedral : 24.405 177.205 3993 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Rotamer: Outliers : 4.48 % Allowed : 21.49 % Favored : 74.03 % 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: -0.23 (0.30), residues: 789 helix: 1.18 (0.27), residues: 382 sheet: -2.32 (0.57), residues: 64 loop : -1.24 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 388 HIS 0.010 0.002 HIS C 962 PHE 0.014 0.002 PHE C 849 TYR 0.014 0.002 TYR C 563 ARG 0.010 0.001 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05895 ( 444) hydrogen bonds : angle 4.48452 ( 1133) metal coordination : bond 0.01051 ( 4) metal coordination : angle 1.62672 ( 3) covalent geometry : bond 0.00581 (11130) covalent geometry : angle 0.68608 (16014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.797 Fit side-chains REVERT: C 309 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6934 (mtmm) REVERT: C 563 TYR cc_start: 0.7687 (m-80) cc_final: 0.7481 (m-80) REVERT: C 703 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: C 971 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8491 (tppt) REVERT: C 994 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8266 (mmmt) REVERT: C 1097 MET cc_start: 0.8195 (tpt) cc_final: 0.7931 (tpp) REVERT: C 1105 MET cc_start: 0.8386 (ppp) cc_final: 0.7803 (ppp) outliers start: 30 outliers final: 14 residues processed: 103 average time/residue: 0.2592 time to fit residues: 37.1929 Evaluate side-chains 88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS C 598 ASN C 659 ASN C 868 HIS ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.175628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116193 restraints weight = 21808.387| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.75 r_work: 0.3415 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11134 Z= 0.113 Angle : 0.575 10.255 16017 Z= 0.287 Chirality : 0.035 0.252 1942 Planarity : 0.004 0.051 1316 Dihedral : 24.287 177.417 3993 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.99 % Allowed : 22.84 % Favored : 74.18 % 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: 0.13 (0.31), residues: 789 helix: 1.47 (0.28), residues: 389 sheet: -2.09 (0.59), residues: 64 loop : -1.12 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 388 HIS 0.008 0.001 HIS C 955 PHE 0.011 0.001 PHE C 597 TYR 0.014 0.002 TYR C 626 ARG 0.006 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 444) hydrogen bonds : angle 4.06092 ( 1133) metal coordination : bond 0.00806 ( 4) metal coordination : angle 1.21468 ( 3) covalent geometry : bond 0.00244 (11130) covalent geometry : angle 0.57525 (16014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: C 455 ARG cc_start: 0.8129 (tpm170) cc_final: 0.7705 (mmm160) REVERT: C 971 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8502 (tppt) REVERT: C 994 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8188 (mmmt) REVERT: C 1011 GLN cc_start: 0.8355 (tt0) cc_final: 0.8068 (tt0) REVERT: C 1105 MET cc_start: 0.8115 (ppp) cc_final: 0.7369 (ppp) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.2734 time to fit residues: 37.1211 Evaluate side-chains 86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS C1016 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.172448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112570 restraints weight = 21996.184| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.06 r_work: 0.3295 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11134 Z= 0.217 Angle : 0.652 10.183 16017 Z= 0.328 Chirality : 0.038 0.250 1942 Planarity : 0.005 0.051 1316 Dihedral : 24.427 177.344 3993 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Rotamer: Outliers : 4.63 % Allowed : 21.79 % Favored : 73.58 % 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: -0.14 (0.31), residues: 789 helix: 1.27 (0.27), residues: 383 sheet: -2.36 (0.56), residues: 69 loop : -1.17 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 388 HIS 0.011 0.002 HIS C 962 PHE 0.011 0.002 PHE C 849 TYR 0.011 0.002 TYR C 626 ARG 0.004 0.001 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05576 ( 444) hydrogen bonds : angle 4.24566 ( 1133) metal coordination : bond 0.00396 ( 4) metal coordination : angle 1.70047 ( 3) covalent geometry : bond 0.00494 (11130) covalent geometry : angle 0.65142 (16014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7507 (mtmm) cc_final: 0.7132 (mtmm) REVERT: C 395 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: C 572 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7608 (p) REVERT: C 703 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: C 994 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8001 (mmmt) REVERT: C 1105 MET cc_start: 0.8341 (ppp) cc_final: 0.7623 (ppp) outliers start: 31 outliers final: 21 residues processed: 102 average time/residue: 0.2663 time to fit residues: 38.2194 Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.175304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114623 restraints weight = 22014.268| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.80 r_work: 0.3390 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11134 Z= 0.118 Angle : 0.580 10.191 16017 Z= 0.290 Chirality : 0.036 0.247 1942 Planarity : 0.004 0.053 1316 Dihedral : 24.333 177.392 3993 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 4.48 % Allowed : 22.84 % Favored : 72.69 % 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: 0.21 (0.31), residues: 789 helix: 1.57 (0.28), residues: 383 sheet: -2.10 (0.57), residues: 69 loop : -1.04 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 388 HIS 0.005 0.001 HIS C 955 PHE 0.008 0.001 PHE C 597 TYR 0.010 0.001 TYR C 626 ARG 0.007 0.000 ARG C1017 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 444) hydrogen bonds : angle 3.97685 ( 1133) metal coordination : bond 0.00958 ( 4) metal coordination : angle 1.11373 ( 3) covalent geometry : bond 0.00256 (11130) covalent geometry : angle 0.58007 (16014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: C 388 TRP cc_start: 0.7165 (m-10) cc_final: 0.6753 (m-10) REVERT: C 395 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: C 428 MET cc_start: 0.6526 (mtp) cc_final: 0.5896 (tpp) REVERT: C 455 ARG cc_start: 0.8061 (tpm170) cc_final: 0.7544 (mmm160) REVERT: C 572 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7531 (p) REVERT: C 868 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8161 (m90) REVERT: C 971 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8612 (tppt) REVERT: C 994 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7958 (mmmt) REVERT: C 1011 GLN cc_start: 0.8401 (tt0) cc_final: 0.8158 (tt0) REVERT: C 1105 MET cc_start: 0.8211 (ppp) cc_final: 0.7438 (ppp) outliers start: 30 outliers final: 17 residues processed: 104 average time/residue: 0.3788 time to fit residues: 56.2849 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.170291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107549 restraints weight = 21904.762| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.79 r_work: 0.3309 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11134 Z= 0.268 Angle : 0.691 10.062 16017 Z= 0.346 Chirality : 0.040 0.259 1942 Planarity : 0.005 0.052 1316 Dihedral : 24.496 177.459 3993 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 4.48 % Allowed : 23.58 % Favored : 71.94 % 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: -0.22 (0.31), residues: 789 helix: 1.24 (0.27), residues: 381 sheet: -2.38 (0.57), residues: 69 loop : -1.25 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 388 HIS 0.010 0.002 HIS C 962 PHE 0.014 0.002 PHE C 849 TYR 0.012 0.002 TYR C 703 ARG 0.006 0.001 ARG C 400 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 444) hydrogen bonds : angle 4.29130 ( 1133) metal coordination : bond 0.00726 ( 4) metal coordination : angle 1.98004 ( 3) covalent geometry : bond 0.00615 (11130) covalent geometry : angle 0.69064 (16014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7275 (mtmm) cc_final: 0.6719 (mtmm) REVERT: C 388 TRP cc_start: 0.7204 (m-10) cc_final: 0.6903 (m-10) REVERT: C 395 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: C 428 MET cc_start: 0.6377 (mtp) cc_final: 0.5747 (tpt) REVERT: C 572 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7657 (p) REVERT: C 703 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: C 994 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7953 (mmmt) REVERT: C 1011 GLN cc_start: 0.8444 (tt0) cc_final: 0.8183 (tt0) REVERT: C 1101 ARG cc_start: 0.7697 (tpt170) cc_final: 0.7475 (tpt170) REVERT: C 1105 MET cc_start: 0.8400 (ppp) cc_final: 0.7547 (ppp) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.3269 time to fit residues: 44.2406 Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 598 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.172895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111866 restraints weight = 21921.947| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.82 r_work: 0.3358 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11134 Z= 0.144 Angle : 0.611 10.249 16017 Z= 0.303 Chirality : 0.037 0.266 1942 Planarity : 0.004 0.053 1316 Dihedral : 24.451 177.450 3993 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 4.03 % Allowed : 23.73 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.31), residues: 789 helix: 1.40 (0.28), residues: 383 sheet: -2.09 (0.59), residues: 69 loop : -1.12 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.008 0.001 PHE C 597 TYR 0.011 0.002 TYR C 350 ARG 0.004 0.000 ARG C 400 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 444) hydrogen bonds : angle 4.05387 ( 1133) metal coordination : bond 0.00823 ( 4) metal coordination : angle 1.51675 ( 3) covalent geometry : bond 0.00323 (11130) covalent geometry : angle 0.61036 (16014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: C 388 TRP cc_start: 0.7367 (m-10) cc_final: 0.7065 (m-10) REVERT: C 395 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: C 428 MET cc_start: 0.6391 (mtp) cc_final: 0.5725 (tpt) REVERT: C 455 ARG cc_start: 0.8082 (tpm170) cc_final: 0.7552 (mmm160) REVERT: C 572 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7583 (p) REVERT: C 601 MET cc_start: 0.8152 (tpp) cc_final: 0.7947 (tpp) REVERT: C 703 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5702 (m-80) REVERT: C 868 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (m90) REVERT: C 902 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8633 (t0) REVERT: C 994 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7906 (mmmt) REVERT: C 1011 GLN cc_start: 0.8408 (tt0) cc_final: 0.8168 (tt0) REVERT: C 1101 ARG cc_start: 0.7578 (tpt170) cc_final: 0.7374 (tpt170) REVERT: C 1105 MET cc_start: 0.8288 (ppp) cc_final: 0.7431 (ppp) outliers start: 27 outliers final: 20 residues processed: 89 average time/residue: 0.3154 time to fit residues: 40.1833 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1016 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.175784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115396 restraints weight = 22164.862| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.69 r_work: 0.3446 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11134 Z= 0.109 Angle : 0.589 9.942 16017 Z= 0.292 Chirality : 0.035 0.214 1942 Planarity : 0.004 0.053 1316 Dihedral : 24.293 177.446 3993 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 2.54 % Allowed : 25.22 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.31), residues: 789 helix: 1.58 (0.28), residues: 381 sheet: -1.67 (0.58), residues: 69 loop : -1.06 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 388 HIS 0.007 0.001 HIS C 718 PHE 0.013 0.001 PHE C 749 TYR 0.011 0.001 TYR C1070 ARG 0.004 0.000 ARG C1001 Details of bonding type rmsd hydrogen bonds : bond 0.05470 ( 444) hydrogen bonds : angle 3.81158 ( 1133) metal coordination : bond 0.01266 ( 4) metal coordination : angle 1.43515 ( 3) covalent geometry : bond 0.00234 (11130) covalent geometry : angle 0.58867 (16014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7446 (mtmm) cc_final: 0.6552 (mmtt) REVERT: C 388 TRP cc_start: 0.7348 (m-10) cc_final: 0.7011 (m-10) REVERT: C 395 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: C 428 MET cc_start: 0.6132 (mtp) cc_final: 0.5538 (tpt) REVERT: C 455 ARG cc_start: 0.7992 (tpm170) cc_final: 0.7388 (mmm160) REVERT: C 601 MET cc_start: 0.8149 (tpp) cc_final: 0.7911 (tpp) REVERT: C 868 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8087 (m90) REVERT: C 994 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7754 (mmmt) REVERT: C 1105 MET cc_start: 0.8182 (ppp) cc_final: 0.7274 (ppp) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.3774 time to fit residues: 51.3713 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 36 optimal weight: 0.0170 chunk 77 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 963 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.176951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119186 restraints weight = 22122.688| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.02 r_work: 0.3425 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11134 Z= 0.105 Angle : 0.588 10.516 16017 Z= 0.289 Chirality : 0.035 0.207 1942 Planarity : 0.004 0.052 1316 Dihedral : 24.214 177.454 3993 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 2.24 % Allowed : 25.37 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.31), residues: 789 helix: 1.70 (0.28), residues: 375 sheet: -1.54 (0.58), residues: 69 loop : -1.10 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 388 HIS 0.006 0.001 HIS C 955 PHE 0.011 0.001 PHE C 749 TYR 0.011 0.001 TYR C1070 ARG 0.003 0.000 ARG C1001 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 444) hydrogen bonds : angle 3.76941 ( 1133) metal coordination : bond 0.01371 ( 4) metal coordination : angle 1.39574 ( 3) covalent geometry : bond 0.00222 (11130) covalent geometry : angle 0.58788 (16014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6491 (mmtt) REVERT: C 388 TRP cc_start: 0.7341 (m-10) cc_final: 0.6969 (m-10) REVERT: C 395 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: C 428 MET cc_start: 0.6159 (mtp) cc_final: 0.5564 (tpt) REVERT: C 455 ARG cc_start: 0.7911 (tpm170) cc_final: 0.7239 (mmm160) REVERT: C 601 MET cc_start: 0.8130 (tpp) cc_final: 0.7907 (tpp) REVERT: C 868 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8130 (m90) REVERT: C 994 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7678 (mmmt) REVERT: C 1105 MET cc_start: 0.8188 (ppp) cc_final: 0.7325 (ppp) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.3391 time to fit residues: 43.3567 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 9.9990 chunk 77 optimal weight: 0.0050 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 963 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.176764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116898 restraints weight = 22287.500| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.01 r_work: 0.3423 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11134 Z= 0.116 Angle : 0.586 10.037 16017 Z= 0.290 Chirality : 0.035 0.206 1942 Planarity : 0.005 0.062 1316 Dihedral : 24.178 177.552 3993 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 2.24 % Allowed : 25.67 % Favored : 72.09 % 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: 0.34 (0.31), residues: 789 helix: 1.72 (0.28), residues: 376 sheet: -1.72 (0.57), residues: 69 loop : -1.05 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 388 HIS 0.006 0.001 HIS C1023 PHE 0.008 0.001 PHE C 749 TYR 0.009 0.001 TYR C1070 ARG 0.004 0.000 ARG C1001 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 444) hydrogen bonds : angle 3.79945 ( 1133) metal coordination : bond 0.00929 ( 4) metal coordination : angle 1.13421 ( 3) covalent geometry : bond 0.00257 (11130) covalent geometry : angle 0.58568 (16014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7491.03 seconds wall clock time: 136 minutes 44.51 seconds (8204.51 seconds total)