Starting phenix.real_space_refine on Wed Sep 17 22:50:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyo_43673/09_2025/8vyo_43673.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 34 5.16 5 C 3818 2.51 5 N 1038 2.21 5 O 1142 1.98 5 H 6039 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12075 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 5009 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 4 Chain: "B" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3589 Classifications: {'peptide': 223} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3475 Classifications: {'peptide': 218} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 236 SG CYS A 248 50.472 42.917 50.745 1.00 89.46 S ATOM 279 SG CYS A 251 51.735 43.151 47.111 1.00 97.16 S ATOM 462 SG CYS A 261 46.788 48.902 61.308 1.00 94.52 S ATOM 504 SG CYS A 264 45.432 51.693 60.944 1.00 97.46 S Time building chain proxies: 1.96, per 1000 atoms: 0.16 Number of scatterers: 12075 At special positions: 0 Unit cell: (75.9, 89.1, 103.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 34 16.00 P 2 15.00 O 1142 8.00 N 1038 7.00 C 3818 6.00 H 6039 1.00 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: 1.20 Conformation dependent library (CDL) restraints added in 292.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 235 " 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 69.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.640A pdb=" N HIS A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 636 through 652 removed outlier: 3.510A pdb=" N TYR A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 671 removed outlier: 4.629A pdb=" N PHE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 removed outlier: 3.730A pdb=" N VAL A 681 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.761A pdb=" N GLU A 703 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 724 removed outlier: 3.632A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.593A pdb=" N GLN B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 3.918A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 66 removed outlier: 4.254A pdb=" N ARG B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 removed outlier: 3.595A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 109 Processing helix chain 'B' and resid 111 through 133 removed outlier: 3.511A pdb=" N LYS B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 160 removed outlier: 4.289A pdb=" N LYS B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.523A pdb=" N ALA B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 230 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.711A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.862A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 29 " --> pdb=" O CYS C 25 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 68 removed outlier: 3.999A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 104 removed outlier: 4.228A pdb=" N MET C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 133 removed outlier: 3.625A pdb=" N LEU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 152 removed outlier: 4.002A pdb=" N LYS C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 210 through 229 removed outlier: 3.742A pdb=" N SER C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 241 Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 464 removed outlier: 7.083A pdb=" N GLN A 530 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A 516 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 584 383 hydrogen bonds defined for protein. 1134 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: 2.79 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6026 1.03 - 1.23: 25 1.23 - 1.42: 2537 1.42 - 1.62: 3531 1.62 - 1.82: 55 Bond restraints: 12174 Sorted by residual: bond pdb=" N ASP B 2 " pdb=" H1 ASP B 2 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASP C 2 " pdb=" H1 ASP C 2 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N ASN B 4 " pdb=" H ASN B 4 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N LEU B 6 " pdb=" CA LEU B 6 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.65e+00 ... (remaining 12169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 21264 1.52 - 3.04: 661 3.04 - 4.56: 41 4.56 - 6.08: 10 6.08 - 7.61: 2 Bond angle restraints: 21978 Sorted by residual: angle pdb=" N ASN B 4 " pdb=" CA ASN B 4 " pdb=" C ASN B 4 " ideal model delta sigma weight residual 111.75 106.25 5.50 1.28e+00 6.10e-01 1.85e+01 angle pdb=" CA TYR B 125 " pdb=" CB TYR B 125 " pdb=" CG TYR B 125 " ideal model delta sigma weight residual 113.90 107.05 6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA GLU B 5 " pdb=" C GLU B 5 " pdb=" O GLU B 5 " ideal model delta sigma weight residual 120.80 116.93 3.87 1.05e+00 9.07e-01 1.36e+01 angle pdb=" C LEU B 6 " pdb=" N VAL B 7 " pdb=" CA VAL B 7 " ideal model delta sigma weight residual 120.30 125.60 -5.30 1.64e+00 3.72e-01 1.04e+01 angle pdb=" CA LEU B 6 " pdb=" C LEU B 6 " pdb=" O LEU B 6 " ideal model delta sigma weight residual 120.63 117.47 3.16 1.08e+00 8.57e-01 8.57e+00 ... (remaining 21973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5205 17.79 - 35.59: 323 35.59 - 53.38: 87 53.38 - 71.18: 67 71.18 - 88.97: 12 Dihedral angle restraints: 5694 sinusoidal: 3116 harmonic: 2578 Sorted by residual: dihedral pdb=" CA THR C 205 " pdb=" C THR C 205 " pdb=" N LEU C 206 " pdb=" CA LEU C 206 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA GLN C 111 " pdb=" C GLN C 111 " pdb=" N ALA C 112 " pdb=" CA ALA C 112 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU A 703 " pdb=" C GLU A 703 " pdb=" N ARG A 704 " pdb=" CA ARG A 704 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 609 0.038 - 0.076: 242 0.076 - 0.114: 43 0.114 - 0.152: 15 0.152 - 0.190: 3 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LEU B 6 " pdb=" N LEU B 6 " pdb=" C LEU B 6 " pdb=" CB LEU B 6 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA GLN C 111 " pdb=" N GLN C 111 " pdb=" C GLN C 111 " pdb=" CB GLN C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA TYR C 125 " pdb=" N TYR C 125 " pdb=" C TYR C 125 " pdb=" CB TYR C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 909 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 4 " -0.199 2.00e-02 2.50e+03 4.13e-01 2.56e+03 pdb=" CG ASN B 4 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 4 " 0.192 2.00e-02 2.50e+03 pdb=" ND2 ASN B 4 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 4 " -0.694 2.00e-02 2.50e+03 pdb="HD22 ASN B 4 " 0.681 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 56 " -0.008 9.50e-02 1.11e+02 4.41e-02 4.36e+01 pdb=" NE ARG C 56 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 56 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 56 " -0.082 2.00e-02 2.50e+03 pdb=" NH2 ARG C 56 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG C 56 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 56 " 0.084 2.00e-02 2.50e+03 pdb="HH21 ARG C 56 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 56 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 127 " -0.007 9.50e-02 1.11e+02 3.62e-02 2.95e+01 pdb=" NE ARG B 127 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG B 127 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 127 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG B 127 " 0.053 2.00e-02 2.50e+03 pdb="HH11 ARG B 127 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 127 " 0.056 2.00e-02 2.50e+03 pdb="HH21 ARG B 127 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 127 " -0.053 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 376 2.12 - 2.74: 22678 2.74 - 3.36: 34851 3.36 - 3.98: 42173 3.98 - 4.60: 68345 Nonbonded interactions: 168423 Sorted by model distance: nonbonded pdb=" OD1 ASP B 124 " pdb=" HH TYR B 149 " model vdw 1.503 2.450 nonbonded pdb=" O GLU C 209 " pdb=" HG SER C 210 " model vdw 1.503 2.450 nonbonded pdb=" OE1 GLN A 653 " pdb=" HG SER A 657 " model vdw 1.540 2.450 nonbonded pdb=" O SER B 210 " pdb=" HG SER B 214 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP A 249 " pdb=" HZ3 LYS A 267 " model vdw 1.569 2.450 ... (remaining 168418 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 69 or resid 73 through 102 or (resid 103 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 104 through 154 or resid 162 through 229)) selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or n \ ame HA )) or resid 6 through 133 or resid 138 through 229)) } 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 group one per residue 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: 1.550 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.005 0.043 6141 Z= 0.259 Angle : 0.725 6.853 8251 Z= 0.437 Chirality : 0.042 0.190 912 Planarity : 0.006 0.055 1051 Dihedral : 13.899 88.973 2327 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.31 % Allowed : 2.29 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.28), residues: 722 helix: -1.21 (0.20), residues: 454 sheet: -1.89 (0.95), residues: 27 loop : -1.11 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG C 56 TYR 0.034 0.005 TYR B 48 PHE 0.015 0.002 PHE C 153 TRP 0.027 0.006 TRP A 619 HIS 0.009 0.003 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 6135) covalent geometry : angle 0.72502 ( 8251) hydrogen bonds : bond 0.20350 ( 383) hydrogen bonds : angle 8.30202 ( 1134) metal coordination : bond 0.00633 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.8777 (tttp) cc_final: 0.8535 (ttmt) REVERT: A 545 GLU cc_start: 0.6825 (tt0) cc_final: 0.6530 (tm-30) REVERT: A 716 LEU cc_start: 0.9304 (mt) cc_final: 0.8997 (mt) REVERT: B 108 ASN cc_start: 0.8223 (m110) cc_final: 0.7864 (t0) outliers start: 2 outliers final: 2 residues processed: 189 average time/residue: 0.2332 time to fit residues: 54.5315 Evaluate side-chains 118 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 461 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN B 4 ASN B 144 GLN B 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.127311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097249 restraints weight = 45113.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100422 restraints weight = 19086.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102244 restraints weight = 11290.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103204 restraints weight = 8486.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103729 restraints weight = 7311.664| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6141 Z= 0.210 Angle : 0.705 5.450 8251 Z= 0.400 Chirality : 0.038 0.173 912 Planarity : 0.005 0.046 1051 Dihedral : 6.316 29.858 822 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.98 % Allowed : 12.52 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.29), residues: 722 helix: -0.14 (0.22), residues: 465 sheet: -1.96 (0.69), residues: 42 loop : -1.31 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 558 TYR 0.021 0.002 TYR C 126 PHE 0.015 0.002 PHE A 707 TRP 0.008 0.001 TRP B 228 HIS 0.004 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6135) covalent geometry : angle 0.70460 ( 8251) hydrogen bonds : bond 0.06520 ( 383) hydrogen bonds : angle 5.68288 ( 1134) metal coordination : bond 0.00378 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.7049 (tt0) cc_final: 0.6588 (tm-30) REVERT: A 689 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (tpt) REVERT: B 108 ASN cc_start: 0.8147 (m110) cc_final: 0.7728 (t0) REVERT: C 26 MET cc_start: 0.9051 (tpt) cc_final: 0.8688 (tpt) REVERT: C 222 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8131 (mtp180) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 0.2035 time to fit residues: 35.8943 Evaluate side-chains 115 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 102 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.125282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095740 restraints weight = 46073.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099129 restraints weight = 19313.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100944 restraints weight = 11431.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101926 restraints weight = 8597.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102442 restraints weight = 7421.245| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6141 Z= 0.258 Angle : 0.680 8.521 8251 Z= 0.385 Chirality : 0.037 0.177 912 Planarity : 0.005 0.043 1051 Dihedral : 5.898 27.204 818 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.21 % Allowed : 13.89 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.29), residues: 722 helix: -0.01 (0.23), residues: 469 sheet: -1.86 (0.68), residues: 38 loop : -1.54 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 60 TYR 0.022 0.002 TYR B 125 PHE 0.011 0.001 PHE A 707 TRP 0.008 0.001 TRP B 59 HIS 0.005 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 6135) covalent geometry : angle 0.68029 ( 8251) hydrogen bonds : bond 0.05646 ( 383) hydrogen bonds : angle 5.44757 ( 1134) metal coordination : bond 0.00613 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.7004 (tt0) cc_final: 0.6624 (tm-30) REVERT: A 586 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 687 LYS cc_start: 0.7806 (pttt) cc_final: 0.7461 (pttt) REVERT: C 26 MET cc_start: 0.9058 (tpt) cc_final: 0.8711 (tpt) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.1872 time to fit residues: 28.0932 Evaluate side-chains 118 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 725 HIS ** 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 = 0.3992 r_free = 0.3992 target = 0.127250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097393 restraints weight = 45553.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100837 restraints weight = 19099.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102684 restraints weight = 11378.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103707 restraints weight = 8549.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104191 restraints weight = 7380.101| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6141 Z= 0.152 Angle : 0.589 5.514 8251 Z= 0.328 Chirality : 0.035 0.169 912 Planarity : 0.004 0.046 1051 Dihedral : 5.517 25.973 818 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.75 % Allowed : 15.11 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.30), residues: 722 helix: 0.50 (0.23), residues: 467 sheet: -1.97 (0.63), residues: 38 loop : -1.52 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.023 0.002 TYR C 126 PHE 0.011 0.001 PHE A 707 TRP 0.006 0.001 TRP B 59 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6135) covalent geometry : angle 0.58853 ( 8251) hydrogen bonds : bond 0.04929 ( 383) hydrogen bonds : angle 4.87585 ( 1134) metal coordination : bond 0.00249 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.6980 (tt0) cc_final: 0.6665 (tm-30) REVERT: A 586 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 26 MET cc_start: 0.9033 (tpt) cc_final: 0.8697 (tpt) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.2100 time to fit residues: 31.6502 Evaluate side-chains 112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 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 = 0.3965 r_free = 0.3965 target = 0.125550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096191 restraints weight = 45353.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099294 restraints weight = 19747.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101249 restraints weight = 11714.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102308 restraints weight = 8747.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102810 restraints weight = 7497.644| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6141 Z= 0.223 Angle : 0.611 5.460 8251 Z= 0.344 Chirality : 0.036 0.171 912 Planarity : 0.004 0.047 1051 Dihedral : 5.414 22.540 818 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 15.88 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.30), residues: 722 helix: 0.40 (0.23), residues: 469 sheet: -2.29 (0.76), residues: 28 loop : -1.47 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.020 0.002 TYR C 126 PHE 0.010 0.001 PHE A 707 TRP 0.006 0.001 TRP B 59 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6135) covalent geometry : angle 0.61145 ( 8251) hydrogen bonds : bond 0.04775 ( 383) hydrogen bonds : angle 4.95876 ( 1134) metal coordination : bond 0.00512 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.7007 (tt0) cc_final: 0.6685 (tm-30) REVERT: A 586 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 26 MET cc_start: 0.9073 (tpt) cc_final: 0.8728 (tpt) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.2080 time to fit residues: 29.0669 Evaluate side-chains 112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096971 restraints weight = 45196.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100067 restraints weight = 19455.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101911 restraints weight = 11759.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102894 restraints weight = 8875.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103420 restraints weight = 7677.853| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6141 Z= 0.152 Angle : 0.570 6.053 8251 Z= 0.316 Chirality : 0.034 0.142 912 Planarity : 0.004 0.045 1051 Dihedral : 5.223 25.257 818 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.98 % Allowed : 16.49 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.30), residues: 722 helix: 0.73 (0.23), residues: 466 sheet: -2.28 (0.74), residues: 28 loop : -1.28 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.019 0.002 TYR C 126 PHE 0.011 0.001 PHE A 707 TRP 0.005 0.001 TRP B 59 HIS 0.009 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6135) covalent geometry : angle 0.57003 ( 8251) hydrogen bonds : bond 0.04514 ( 383) hydrogen bonds : angle 4.65981 ( 1134) metal coordination : bond 0.00294 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.6960 (tt0) cc_final: 0.6667 (tm-30) REVERT: A 586 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 108 ASN cc_start: 0.8023 (m-40) cc_final: 0.7295 (t0) REVERT: C 26 MET cc_start: 0.9028 (tpt) cc_final: 0.8636 (tpt) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.2160 time to fit residues: 31.0438 Evaluate side-chains 107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN B 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098034 restraints weight = 44906.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101277 restraints weight = 19188.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103211 restraints weight = 11276.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104218 restraints weight = 8365.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104682 restraints weight = 7172.204| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6141 Z= 0.129 Angle : 0.557 6.487 8251 Z= 0.304 Chirality : 0.035 0.175 912 Planarity : 0.004 0.042 1051 Dihedral : 5.059 25.373 818 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.07 % Allowed : 18.78 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.30), residues: 722 helix: 0.98 (0.23), residues: 467 sheet: -2.15 (0.76), residues: 28 loop : -1.29 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.012 0.002 TYR B 128 PHE 0.011 0.001 PHE A 707 TRP 0.005 0.001 TRP B 59 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6135) covalent geometry : angle 0.55680 ( 8251) hydrogen bonds : bond 0.04279 ( 383) hydrogen bonds : angle 4.46646 ( 1134) metal coordination : bond 0.00252 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.6943 (tt0) cc_final: 0.6713 (tm-30) REVERT: A 564 MET cc_start: 0.8113 (tpp) cc_final: 0.7345 (tpp) REVERT: A 586 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 687 LYS cc_start: 0.7579 (pttt) cc_final: 0.7263 (pttt) REVERT: C 26 MET cc_start: 0.8992 (tpt) cc_final: 0.8638 (tpt) outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 0.1935 time to fit residues: 27.6301 Evaluate side-chains 101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096960 restraints weight = 44796.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100064 restraints weight = 19265.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101945 restraints weight = 11497.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102950 restraints weight = 8615.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103419 restraints weight = 7420.155| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6141 Z= 0.140 Angle : 0.548 5.604 8251 Z= 0.303 Chirality : 0.035 0.154 912 Planarity : 0.004 0.041 1051 Dihedral : 4.939 24.088 818 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.68 % Allowed : 18.32 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.31), residues: 722 helix: 1.08 (0.23), residues: 468 sheet: -2.22 (0.77), residues: 28 loop : -1.26 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.014 0.002 TYR B 125 PHE 0.011 0.001 PHE A 707 TRP 0.005 0.001 TRP B 59 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6135) covalent geometry : angle 0.54814 ( 8251) hydrogen bonds : bond 0.04141 ( 383) hydrogen bonds : angle 4.45286 ( 1134) metal coordination : bond 0.00306 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.7699 (ptm160) REVERT: A 545 GLU cc_start: 0.6927 (tt0) cc_final: 0.6666 (tm-30) REVERT: A 564 MET cc_start: 0.8115 (tpp) cc_final: 0.7324 (tpp) REVERT: A 586 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 687 LYS cc_start: 0.7593 (pttt) cc_final: 0.7260 (pttt) REVERT: B 108 ASN cc_start: 0.8057 (m-40) cc_final: 0.7333 (t0) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.1941 time to fit residues: 26.0305 Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.126494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096600 restraints weight = 44458.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099915 restraints weight = 19228.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101825 restraints weight = 11534.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102738 restraints weight = 8642.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103284 restraints weight = 7469.899| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6141 Z= 0.191 Angle : 0.585 5.655 8251 Z= 0.324 Chirality : 0.035 0.145 912 Planarity : 0.004 0.038 1051 Dihedral : 4.926 21.948 818 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.31), residues: 722 helix: 1.01 (0.23), residues: 466 sheet: -2.38 (0.78), residues: 28 loop : -1.36 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.019 0.002 TYR B 125 PHE 0.010 0.001 PHE A 707 TRP 0.007 0.001 TRP B 228 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6135) covalent geometry : angle 0.58460 ( 8251) hydrogen bonds : bond 0.04156 ( 383) hydrogen bonds : angle 4.56663 ( 1134) metal coordination : bond 0.00535 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7724 (ptm160) REVERT: A 545 GLU cc_start: 0.6922 (tt0) cc_final: 0.6708 (tm-30) REVERT: A 586 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 687 LYS cc_start: 0.7626 (pttt) cc_final: 0.7299 (pttt) REVERT: C 126 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7823 (m-10) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.1918 time to fit residues: 24.6263 Evaluate side-chains 101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 137 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 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 = 0.4011 r_free = 0.4011 target = 0.128020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098039 restraints weight = 44737.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101266 restraints weight = 19221.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103189 restraints weight = 11535.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104139 restraints weight = 8627.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104563 restraints weight = 7445.340| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6141 Z= 0.126 Angle : 0.545 5.471 8251 Z= 0.296 Chirality : 0.035 0.142 912 Planarity : 0.004 0.035 1051 Dihedral : 4.814 25.093 818 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.76 % Allowed : 19.08 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.31), residues: 722 helix: 1.23 (0.24), residues: 466 sheet: -2.42 (0.64), residues: 38 loop : -1.35 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.013 0.002 TYR B 128 PHE 0.011 0.001 PHE A 707 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6135) covalent geometry : angle 0.54539 ( 8251) hydrogen bonds : bond 0.04033 ( 383) hydrogen bonds : angle 4.35318 ( 1134) metal coordination : bond 0.00227 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ARG cc_start: 0.8414 (ttt-90) cc_final: 0.7733 (ptm160) REVERT: A 545 GLU cc_start: 0.6877 (tt0) cc_final: 0.6640 (tm-30) REVERT: A 555 ASP cc_start: 0.8405 (t70) cc_final: 0.8197 (m-30) REVERT: A 586 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 687 LYS cc_start: 0.7609 (pttt) cc_final: 0.7265 (pttt) REVERT: C 126 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7590 (m-80) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.1923 time to fit residues: 23.8369 Evaluate side-chains 96 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 126 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.127775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097940 restraints weight = 44229.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101222 restraints weight = 18908.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103098 restraints weight = 11340.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104120 restraints weight = 8499.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104544 restraints weight = 7305.981| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6141 Z= 0.137 Angle : 0.551 6.672 8251 Z= 0.298 Chirality : 0.035 0.190 912 Planarity : 0.004 0.035 1051 Dihedral : 4.717 23.879 818 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.07 % Allowed : 19.54 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.31), residues: 722 helix: 1.26 (0.24), residues: 466 sheet: -2.39 (0.65), residues: 38 loop : -1.35 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.011 0.001 TYR B 211 PHE 0.011 0.001 PHE A 707 TRP 0.005 0.001 TRP B 59 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6135) covalent geometry : angle 0.55095 ( 8251) hydrogen bonds : bond 0.03950 ( 383) hydrogen bonds : angle 4.34447 ( 1134) metal coordination : bond 0.00294 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.24 seconds wall clock time: 40 minutes 31.52 seconds (2431.52 seconds total)