Starting phenix.real_space_refine on Thu Aug 6 23:08:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443.map" model { file = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2026/8up5_42443_neut.cif" } resolution = 3.56 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= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6767 atoms to isotropic. 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 P 73 5.49 5 S 22 5.16 5 C 4076 2.51 5 N 1180 2.21 5 O 1459 1.98 5 H 5818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 5 Chain: "T" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 2326 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 60} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2614 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 7, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "K" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4658 Classifications: {'peptide': 321} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1954 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 9, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "P" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1076 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.54, per 1000 atoms: 0.20 Number of scatterers: 12628 At special positions: 0 Unit cell: (67.98, 89.61, 131.84, 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) S 22 16.00 P 73 15.00 O 1459 8.00 N 1180 7.00 C 4076 6.00 H 5818 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 361.4 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 54.6% alpha, 13.9% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 369 through 394 removed outlier: 4.426A pdb=" N LYS B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.475A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.751A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.928A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.542A pdb=" N VAL B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 3.720A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'K' and resid 43 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 153 through 165 Processing helix chain 'K' and resid 171 through 182 removed outlier: 3.586A pdb=" N LYS K 181 " --> pdb=" O GLU K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 212 removed outlier: 4.333A pdb=" N LEU K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 271 Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.306A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 3.996A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.940A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.651A pdb=" N VAL C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.272A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 109 through 112 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'P' and resid 16 through 33 removed outlier: 3.925A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 80 removed outlier: 3.796A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 361 removed outlier: 3.816A pdb=" N ASP B 403 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 removed outlier: 3.523A pdb=" N LYS B 419 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AA4, first strand: chain 'K' and resid 23 through 31 removed outlier: 5.765A pdb=" N VAL K 24 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR K 19 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE K 2 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA K 72 " --> pdb=" O ILE K 2 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU K 4 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER K 74 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU K 6 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLY K 76 " --> pdb=" O LEU K 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 142 through 148 removed outlier: 4.934A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL K 139 " --> pdb=" O TYR K 143 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL K 145 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA K 137 " --> pdb=" O VAL K 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY K 147 " --> pdb=" O VAL K 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.102A pdb=" N GLY C 84 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 13 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 8 through 13 321 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5757 1.03 - 1.23: 82 1.23 - 1.42: 3063 1.42 - 1.61: 3954 1.61 - 1.81: 39 Bond restraints: 12895 Sorted by residual: bond pdb=" N ASP B 467 " pdb=" H ASP B 467 " ideal model delta sigma weight residual 0.860 1.185 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" N SER K 129 " pdb=" H SER K 129 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" N ILE B 466 " pdb=" H ILE B 466 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N GLY K 131 " pdb=" H GLY K 131 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N GLY K 130 " pdb=" H GLY K 130 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 ... (remaining 12890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 22915 2.45 - 4.91: 277 4.91 - 7.36: 27 7.36 - 9.81: 8 9.81 - 12.27: 4 Bond angle restraints: 23231 Sorted by residual: angle pdb=" N ARG B 530 " pdb=" CA ARG B 530 " pdb=" C ARG B 530 " ideal model delta sigma weight residual 111.11 122.56 -11.45 1.20e+00 6.94e-01 9.11e+01 angle pdb=" N ARG B 532 " pdb=" CA ARG B 532 " pdb=" C ARG B 532 " ideal model delta sigma weight residual 110.50 121.45 -10.95 1.41e+00 5.03e-01 6.03e+01 angle pdb=" CA THR K 133 " pdb=" C THR K 133 " pdb=" O THR K 133 " ideal model delta sigma weight residual 120.36 113.28 7.08 1.07e+00 8.73e-01 4.37e+01 angle pdb=" N ARG B 532 " pdb=" CA ARG B 532 " pdb=" CB ARG B 532 " ideal model delta sigma weight residual 110.17 101.93 8.24 1.44e+00 4.82e-01 3.28e+01 angle pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " ideal model delta sigma weight residual 111.62 102.36 9.26 1.62e+00 3.81e-01 3.26e+01 ... (remaining 23226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 5771 33.82 - 67.63: 403 67.63 - 101.45: 48 101.45 - 135.26: 3 135.26 - 169.08: 2 Dihedral angle restraints: 6227 sinusoidal: 3872 harmonic: 2355 Sorted by residual: dihedral pdb=" C ILE B 466 " pdb=" N ILE B 466 " pdb=" CA ILE B 466 " pdb=" CB ILE B 466 " ideal model delta harmonic sigma weight residual -122.00 -136.47 14.47 0 2.50e+00 1.60e-01 3.35e+01 dihedral pdb=" O4' C T 74 " pdb=" C1' C T 74 " pdb=" N1 C T 74 " pdb=" C2 C T 74 " ideal model delta sinusoidal sigma weight residual -128.00 -42.70 -85.30 1 1.70e+01 3.46e-03 3.05e+01 dihedral pdb=" C4' C T 74 " pdb=" C3' C T 74 " pdb=" O3' C T 74 " pdb=" P C T 75 " ideal model delta sinusoidal sigma weight residual -110.00 59.08 -169.08 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1122 0.096 - 0.191: 101 0.191 - 0.287: 3 0.287 - 0.382: 1 0.382 - 0.478: 5 Chirality restraints: 1232 Sorted by residual: chirality pdb=" P U T 36 " pdb=" OP1 U T 36 " pdb=" OP2 U T 36 " pdb=" O5' U T 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" P C T 75 " pdb=" OP1 C T 75 " pdb=" OP2 C T 75 " pdb=" O5' C T 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" P C T 74 " pdb=" OP1 C T 74 " pdb=" OP2 C T 74 " pdb=" O5' C T 74 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 1229 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 132 " -0.234 2.00e-02 2.50e+03 3.94e-01 2.33e+03 pdb=" CG ASN K 132 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN K 132 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN K 132 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN K 132 " 0.632 2.00e-02 2.50e+03 pdb="HD22 ASN K 132 " -0.653 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 466 " -0.095 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" N ASP B 467 " 0.262 2.00e-02 2.50e+03 pdb=" CA ASP B 467 " -0.076 2.00e-02 2.50e+03 pdb=" H ASP B 467 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 530 " 0.051 2.00e-02 2.50e+03 8.94e-02 7.98e+01 pdb=" N ALA B 531 " -0.154 2.00e-02 2.50e+03 pdb=" CA ALA B 531 " 0.042 2.00e-02 2.50e+03 pdb=" H ALA B 531 " 0.061 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 27 1.64 - 2.38: 5087 2.38 - 3.12: 38487 3.12 - 3.86: 53813 3.86 - 4.60: 84024 Warning: very small nonbonded interaction distances. Nonbonded interactions: 181438 Sorted by model distance: nonbonded pdb="HD22 ASN K 105 " pdb=" CD2 TYR K 314 " model vdw 0.903 2.240 nonbonded pdb=" OH TYR K 314 " pdb=" CG2 VAL K 319 " model vdw 1.114 3.100 nonbonded pdb="HH21 ARG B 532 " pdb=" HB2 PRO K 77 " model vdw 1.126 2.270 nonbonded pdb=" CG ASN K 105 " pdb=" HE2 TYR K 314 " model vdw 1.127 2.200 nonbonded pdb=" HH TYR K 314 " pdb="HG21 VAL K 319 " model vdw 1.171 2.270 ... (remaining 181433 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 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.350 Find NCS groups from input model: 0.040 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 0.006 0.378 7078 Z= 0.511 Angle : 0.760 11.452 9951 Z= 0.529 Chirality : 0.056 0.478 1232 Planarity : 0.004 0.052 991 Dihedral : 21.347 169.079 3023 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.60 % Allowed : 26.65 % Favored : 72.75 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.41 (0.33), residues: 694 helix: 1.36 (0.29), residues: 349 sheet: 0.05 (0.59), residues: 78 loop : -1.11 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 38 TYR 0.016 0.001 TYR P 36 PHE 0.008 0.001 PHE C 27 TRP 0.007 0.001 TRP K 302 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.24 ( 7077) covalent geometry : angle 0.75987 / 0.53 ( 9951) hydrogen bonds : bond 0.14562 / 15.46 ( 372) hydrogen bonds : angle 6.72820 / 8.50 ( 995) Misc. bond : bond 0.37800 / 18.90 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.349 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 outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.1604 time to fit residues: 19.3275 Evaluate side-chains 84 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 408 ASN B 475 ASN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 ASN C 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.159737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.121495 restraints weight = 32401.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.126368 restraints weight = 17390.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.129569 restraints weight = 11144.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.131664 restraints weight = 8225.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.133082 restraints weight = 6721.026| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7078 Z= 0.195 Angle : 0.556 6.528 9951 Z= 0.311 Chirality : 0.041 0.207 1232 Planarity : 0.004 0.033 991 Dihedral : 21.457 167.729 1924 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.40 % Allowed : 25.65 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.13 (0.32), residues: 694 helix: 1.24 (0.27), residues: 351 sheet: -0.17 (0.58), residues: 77 loop : -1.41 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 532 TYR 0.028 0.002 TYR K 314 PHE 0.014 0.002 PHE B 506 TRP 0.005 0.001 TRP K 291 HIS 0.007 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 7077) covalent geometry : angle 0.55645 / 0.31 ( 9951) hydrogen bonds : bond 0.06877 / 7.17 ( 372) hydrogen bonds : angle 5.64543 / 7.07 ( 995) Misc. bond : bond 0.00902 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.306 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 outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1596 time to fit residues: 20.9559 Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain P residue 9 LYS Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.0070 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.160039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.121696 restraints weight = 32315.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.126596 restraints weight = 17040.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.129839 restraints weight = 10865.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.131928 restraints weight = 7989.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.133077 restraints weight = 6521.187| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7078 Z= 0.143 Angle : 0.504 5.884 9951 Z= 0.283 Chirality : 0.039 0.196 1232 Planarity : 0.003 0.032 991 Dihedral : 21.447 168.519 1922 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.61 % Allowed : 25.65 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.15 (0.32), residues: 694 helix: 1.26 (0.27), residues: 351 sheet: -0.37 (0.56), residues: 77 loop : -1.34 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 315 TYR 0.019 0.002 TYR K 314 PHE 0.032 0.002 PHE C 21 TRP 0.006 0.001 TRP K 291 HIS 0.006 0.001 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7077) covalent geometry : angle 0.50351 / 0.28 ( 9951) hydrogen bonds : bond 0.05995 / 6.21 ( 372) hydrogen bonds : angle 5.36210 / 6.73 ( 995) Misc. bond : bond 0.00250 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 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 outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.1449 time to fit residues: 19.9961 Evaluate side-chains 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121261 restraints weight = 32185.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.126137 restraints weight = 17076.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.129354 restraints weight = 10933.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131356 restraints weight = 8075.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132745 restraints weight = 6626.266| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7078 Z= 0.147 Angle : 0.494 5.146 9951 Z= 0.278 Chirality : 0.039 0.193 1232 Planarity : 0.003 0.033 991 Dihedral : 21.394 168.541 1922 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.01 % Allowed : 26.05 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.12 (0.32), residues: 694 helix: 1.25 (0.27), residues: 351 sheet: -0.37 (0.56), residues: 77 loop : -1.36 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 315 TYR 0.015 0.002 TYR K 314 PHE 0.011 0.001 PHE B 506 TRP 0.008 0.001 TRP K 291 HIS 0.006 0.002 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 7077) covalent geometry : angle 0.49355 / 0.28 ( 9951) hydrogen bonds : bond 0.05652 / 5.77 ( 372) hydrogen bonds : angle 5.22809 / 6.58 ( 995) Misc. bond : bond 0.00411 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.281 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 outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.1526 time to fit residues: 20.2574 Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 ASN C 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.159159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.120781 restraints weight = 32393.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.125630 restraints weight = 17315.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.128812 restraints weight = 11089.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.130884 restraints weight = 8231.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.132242 restraints weight = 6745.778| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7078 Z= 0.152 Angle : 0.495 4.671 9951 Z= 0.279 Chirality : 0.038 0.192 1232 Planarity : 0.004 0.043 991 Dihedral : 21.387 169.317 1922 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.21 % Allowed : 26.45 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.09 (0.32), residues: 694 helix: 1.22 (0.28), residues: 351 sheet: -0.41 (0.55), residues: 77 loop : -1.37 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 315 TYR 0.016 0.002 TYR K 314 PHE 0.011 0.001 PHE B 506 TRP 0.007 0.001 TRP K 291 HIS 0.006 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 7077) covalent geometry : angle 0.49478 / 0.28 ( 9951) hydrogen bonds : bond 0.05598 / 5.71 ( 372) hydrogen bonds : angle 5.16799 / 6.51 ( 995) Misc. bond : bond 0.00466 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.329 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 outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.1374 time to fit residues: 18.1506 Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.160415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121967 restraints weight = 32055.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.126903 restraints weight = 17000.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130205 restraints weight = 10858.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.132320 restraints weight = 7988.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.133386 restraints weight = 6540.627| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7078 Z= 0.117 Angle : 0.474 4.461 9951 Z= 0.266 Chirality : 0.038 0.192 1232 Planarity : 0.003 0.033 991 Dihedral : 21.356 170.727 1922 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.61 % Allowed : 27.45 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.33 (0.32), residues: 694 helix: 1.37 (0.28), residues: 351 sheet: -0.35 (0.56), residues: 77 loop : -1.15 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.016 0.001 TYR K 314 PHE 0.010 0.001 PHE B 468 TRP 0.006 0.001 TRP K 291 HIS 0.006 0.002 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 7077) covalent geometry : angle 0.47431 / 0.27 ( 9951) hydrogen bonds : bond 0.05236 / 5.29 ( 372) hydrogen bonds : angle 4.99879 / 6.28 ( 995) Misc. bond : bond 0.00468 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.322 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: K 51 THR cc_start: 0.6659 (m) cc_final: 0.6429 (m) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.1569 time to fit residues: 20.1067 Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.160611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.122187 restraints weight = 32129.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.127184 restraints weight = 16896.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.130527 restraints weight = 10691.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.132596 restraints weight = 7816.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.133954 restraints weight = 6405.603| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7078 Z= 0.116 Angle : 0.473 4.273 9951 Z= 0.264 Chirality : 0.038 0.189 1232 Planarity : 0.003 0.032 991 Dihedral : 21.314 170.827 1922 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.41 % Allowed : 26.65 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.40 (0.32), residues: 694 helix: 1.43 (0.28), residues: 351 sheet: -0.34 (0.56), residues: 77 loop : -1.11 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.016 0.002 TYR K 314 PHE 0.008 0.001 PHE B 468 TRP 0.006 0.001 TRP K 291 HIS 0.006 0.001 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 7077) covalent geometry : angle 0.47302 / 0.26 ( 9951) hydrogen bonds : bond 0.05170 / 5.19 ( 372) hydrogen bonds : angle 4.93035 / 6.20 ( 995) Misc. bond : bond 0.00494 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.308 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: K 51 THR cc_start: 0.6628 (m) cc_final: 0.6385 (m) outliers start: 17 outliers final: 14 residues processed: 95 average time/residue: 0.1585 time to fit residues: 20.8848 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.159719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121219 restraints weight = 32208.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.126065 restraints weight = 17187.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.129265 restraints weight = 11035.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131314 restraints weight = 8196.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.132608 restraints weight = 6741.959| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7078 Z= 0.144 Angle : 0.487 4.841 9951 Z= 0.273 Chirality : 0.038 0.189 1232 Planarity : 0.003 0.031 991 Dihedral : 21.291 170.750 1922 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.41 % Allowed : 26.65 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.25 (0.32), residues: 694 helix: 1.34 (0.28), residues: 351 sheet: -0.40 (0.55), residues: 77 loop : -1.25 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.016 0.002 TYR K 314 PHE 0.007 0.001 PHE B 506 TRP 0.006 0.001 TRP K 302 HIS 0.005 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7077) covalent geometry : angle 0.48665 / 0.27 ( 9951) hydrogen bonds : bond 0.05358 / 5.37 ( 372) hydrogen bonds : angle 4.93758 / 6.23 ( 995) Misc. bond : bond 0.00500 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.311 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: B 362 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5283 (mtt90) REVERT: K 51 THR cc_start: 0.6586 (m) cc_final: 0.6345 (m) REVERT: C 60 MET cc_start: 0.4728 (ttm) cc_final: 0.4447 (tmm) REVERT: C 140 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6879 (tt0) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.1523 time to fit residues: 19.7847 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.158090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.120235 restraints weight = 32421.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.124839 restraints weight = 17569.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.127923 restraints weight = 11436.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.129832 restraints weight = 8525.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.131167 restraints weight = 7044.920| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7078 Z= 0.171 Angle : 0.503 3.972 9951 Z= 0.284 Chirality : 0.039 0.190 1232 Planarity : 0.004 0.036 991 Dihedral : 21.311 171.036 1922 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.01 % Allowed : 25.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: -0.00 (0.32), residues: 694 helix: 1.16 (0.27), residues: 351 sheet: -0.45 (0.55), residues: 77 loop : -1.43 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 84 TYR 0.021 0.002 TYR K 127 PHE 0.013 0.002 PHE B 506 TRP 0.007 0.001 TRP K 302 HIS 0.008 0.002 HIS K 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7077) covalent geometry : angle 0.50305 / 0.28 ( 9951) hydrogen bonds : bond 0.05616 / 5.67 ( 372) hydrogen bonds : angle 5.01186 / 6.34 ( 995) Misc. bond : bond 0.00522 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.315 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: B 362 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5298 (mtt90) outliers start: 20 outliers final: 16 residues processed: 94 average time/residue: 0.1522 time to fit residues: 20.2286 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.121049 restraints weight = 32441.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.125669 restraints weight = 17469.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.128768 restraints weight = 11344.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130812 restraints weight = 8464.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.132001 restraints weight = 6953.551| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7078 Z= 0.140 Angle : 0.495 4.459 9951 Z= 0.277 Chirality : 0.039 0.192 1232 Planarity : 0.004 0.032 991 Dihedral : 21.309 171.967 1922 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.61 % Allowed : 26.25 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.16 (0.32), residues: 694 helix: 1.26 (0.28), residues: 351 sheet: -0.41 (0.56), residues: 77 loop : -1.29 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.017 0.002 TYR K 314 PHE 0.009 0.001 PHE B 468 TRP 0.007 0.001 TRP K 302 HIS 0.005 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 7077) covalent geometry : angle 0.49537 / 0.28 ( 9951) hydrogen bonds : bond 0.05391 / 5.43 ( 372) hydrogen bonds : angle 4.92136 / 6.21 ( 995) Misc. bond : bond 0.00516 / 0.26 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue ILE 465 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.316 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: B 362 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5267 (mtt90) REVERT: K 51 THR cc_start: 0.6588 (m) cc_final: 0.6355 (m) REVERT: C 140 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6867 (tt0) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1522 time to fit residues: 20.0072 Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.3698 > 50:) chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.159295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.121398 restraints weight = 32369.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.126047 restraints weight = 17444.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.129241 restraints weight = 11319.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.131181 restraints weight = 8377.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.132562 restraints weight = 6914.209| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7078 Z= 0.129 Angle : 0.492 4.499 9951 Z= 0.275 Chirality : 0.039 0.192 1232 Planarity : 0.003 0.030 991 Dihedral : 21.284 172.159 1922 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.21 % Allowed : 26.65 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.25 (0.32), residues: 694 helix: 1.28 (0.28), residues: 353 sheet: -0.27 (0.56), residues: 77 loop : -1.21 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.029 0.002 TYR P 36 PHE 0.008 0.001 PHE B 468 TRP 0.007 0.001 TRP K 302 HIS 0.006 0.001 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7077) covalent geometry : angle 0.49216 / 0.27 ( 9951) hydrogen bonds : bond 0.05247 / 5.28 ( 372) hydrogen bonds : angle 4.86242 / 6.13 ( 995) Misc. bond : bond 0.00526 / 0.26 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.53 seconds wall clock time: 44 minutes 42.30 seconds (2682.30 seconds total)