Starting phenix.real_space_refine on Sat Jul 4 02:58:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up5_42443/07_2026/8up5_42443_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up5_42443/07_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_42443/07_2026/8up5_42443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up5_42443/07_2026/8up5_42443.map" model { file = "/net/cci-nas-00/data/ceres_data/8up5_42443/07_2026/8up5_42443_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up5_42443/07_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-dev-6108/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: 2.40, per 1000 atoms: 0.19 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: 1.27 Conformation dependent library (CDL) restraints added in 373.9 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: 2.24 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: 3.02 Time building geometry restraints manager: 1.69 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: 278 4.91 - 7.36: 26 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=" O3' U T 36 " pdb=" C3' U T 36 " pdb=" C2' U T 36 " ideal model delta sigma weight residual 109.50 119.65 -10.15 1.50e+00 4.44e-01 4.58e+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 ... (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: 1170 0.096 - 0.191: 53 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: 1.290 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- 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= 0.504 Angle : 0.713 11.452 9951 Z= 0.476 Chirality : 0.051 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 0.00377 / 0.23 ( 7077) covalent geometry : angle 0.71348 / 0.48 ( 9951) hydrogen bonds : bond 0.14562 / 14.38 ( 372) hydrogen bonds : angle 6.72820 / 8.03 ( 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 : 0.305 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: 0.1552 time to fit residues: 18.0692 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 : 0.278 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.159585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.121405 restraints weight = 32277.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.126203 restraints weight = 17194.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.129360 restraints weight = 11020.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.131437 restraints weight = 8141.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132610 restraints weight = 6669.675| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7078 Z= 0.195 Angle : 0.547 4.195 9951 Z= 0.313 Chirality : 0.039 0.138 1232 Planarity : 0.004 0.038 991 Dihedral : 21.637 166.778 1924 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.61 % Allowed : 25.45 % 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: 0.10 (0.32), residues: 694 helix: 1.22 (0.27), residues: 351 sheet: -0.19 (0.58), residues: 77 loop : -1.42 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 37 TYR 0.025 0.002 TYR K 314 PHE 0.014 0.002 PHE B 506 TRP 0.005 0.001 TRP K 291 HIS 0.008 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7077) covalent geometry : angle 0.54724 / 0.31 ( 9951) hydrogen bonds : bond 0.06716 / 6.45 ( 372) hydrogen bonds : angle 5.63423 / 6.71 ( 995) Misc. bond : bond 0.00676 / 0.34 ( 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 102 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1637 time to fit residues: 21.7504 Evaluate side-chains 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.159723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.121252 restraints weight = 32292.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.126168 restraints weight = 17144.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.129409 restraints weight = 10944.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.131494 restraints weight = 8048.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132842 restraints weight = 6591.884| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.1109 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= 0.146 Angle : 0.488 4.301 9951 Z= 0.281 Chirality : 0.038 0.140 1232 Planarity : 0.003 0.034 991 Dihedral : 21.612 169.048 1922 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.32 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: 0.08 (0.32), residues: 694 helix: 1.23 (0.27), residues: 351 sheet: -0.42 (0.56), residues: 77 loop : -1.40 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 315 TYR 0.015 0.002 TYR K 314 PHE 0.022 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 0.00307 / 0.15 ( 7077) covalent geometry : angle 0.48783 / 0.28 ( 9951) hydrogen bonds : bond 0.05884 / 5.58 ( 372) hydrogen bonds : angle 5.34690 / 6.35 ( 995) Misc. bond : bond 0.00875 / 0.44 ( 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 105 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.301 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: 0.1314 time to fit residues: 18.0133 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain C residue 140 GLU 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: 1.9990 chunk 1 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.158631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.120573 restraints weight = 32368.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.125209 restraints weight = 17726.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.128227 restraints weight = 11550.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.130296 restraints weight = 8636.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.131421 restraints weight = 7116.994| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7078 Z= 0.179 Angle : 0.501 3.761 9951 Z= 0.289 Chirality : 0.038 0.140 1232 Planarity : 0.004 0.034 991 Dihedral : 21.581 167.902 1922 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.41 % Allowed : 25.65 % 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: -0.10 (0.31), residues: 694 helix: 1.08 (0.27), residues: 351 sheet: -0.42 (0.56), residues: 77 loop : -1.51 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 84 TYR 0.017 0.002 TYR K 314 PHE 0.017 0.002 PHE C 21 TRP 0.007 0.001 TRP K 291 HIS 0.005 0.002 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 7077) covalent geometry : angle 0.50139 / 0.29 ( 9951) hydrogen bonds : bond 0.05827 / 5.51 ( 372) hydrogen bonds : angle 5.30160 / 6.33 ( 995) Misc. bond : bond 0.00168 / 0.08 ( 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: 17 poor density : 83 time to evaluate : 0.285 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 106 HIS cc_start: 0.6444 (t70) cc_final: 0.5964 (t-170) outliers start: 17 outliers final: 15 residues processed: 93 average time/residue: 0.1348 time to fit residues: 17.7484 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 2 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 10.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.157046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.119143 restraints weight = 32742.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123661 restraints weight = 17968.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.126654 restraints weight = 11780.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.128568 restraints weight = 8850.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.129837 restraints weight = 7335.353| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7078 Z= 0.209 Angle : 0.523 4.532 9951 Z= 0.302 Chirality : 0.039 0.139 1232 Planarity : 0.004 0.051 991 Dihedral : 21.607 168.526 1922 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.01 % Allowed : 26.65 % Favored : 69.34 % 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: -0.46 (0.31), residues: 694 helix: 0.82 (0.27), residues: 351 sheet: -0.62 (0.56), residues: 77 loop : -1.72 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 91 TYR 0.019 0.002 TYR K 190 PHE 0.015 0.002 PHE B 506 TRP 0.006 0.001 TRP K 291 HIS 0.005 0.002 HIS K 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 7077) covalent geometry : angle 0.52347 / 0.30 ( 9951) hydrogen bonds : bond 0.06055 / 5.80 ( 372) hydrogen bonds : angle 5.35186 / 6.42 ( 995) Misc. bond : bond 0.00249 / 0.12 ( 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 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.4930 (ttm) cc_final: 0.4594 (tmm) REVERT: C 140 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6852 (tt0) outliers start: 20 outliers final: 16 residues processed: 92 average time/residue: 0.1409 time to fit residues: 18.4019 Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 262 MET 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: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120602 restraints weight = 32353.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.125313 restraints weight = 17235.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.128554 restraints weight = 11061.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130597 restraints weight = 8195.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.131621 restraints weight = 6726.323| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7078 Z= 0.138 Angle : 0.482 4.167 9951 Z= 0.278 Chirality : 0.038 0.143 1232 Planarity : 0.004 0.036 991 Dihedral : 21.595 170.379 1922 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.01 % Allowed : 27.25 % Favored : 69.74 % 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: 1.02 (0.28), residues: 351 sheet: -0.60 (0.55), residues: 77 loop : -1.44 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.017 0.002 TYR K 314 PHE 0.011 0.001 PHE B 468 TRP 0.007 0.001 TRP K 291 HIS 0.006 0.002 HIS K 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7077) covalent geometry : angle 0.48238 / 0.28 ( 9951) hydrogen bonds : bond 0.05496 / 5.18 ( 372) hydrogen bonds : angle 5.12331 / 6.11 ( 995) Misc. bond : bond 0.00623 / 0.31 ( 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 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 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 outliers start: 15 outliers final: 14 residues processed: 94 average time/residue: 0.1528 time to fit residues: 20.2556 Evaluate side-chains 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.157925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.119988 restraints weight = 32680.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.124586 restraints weight = 17799.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.127671 restraints weight = 11593.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.129633 restraints weight = 8667.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130807 restraints weight = 7157.556| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7078 Z= 0.164 Angle : 0.492 3.788 9951 Z= 0.283 Chirality : 0.038 0.139 1232 Planarity : 0.004 0.034 991 Dihedral : 21.567 169.707 1922 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.81 % Allowed : 27.05 % Favored : 69.14 % 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: -0.23 (0.31), residues: 694 helix: 0.96 (0.27), residues: 351 sheet: -0.61 (0.56), residues: 77 loop : -1.51 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.018 0.002 TYR K 314 PHE 0.011 0.002 PHE B 506 TRP 0.006 0.001 TRP K 302 HIS 0.006 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7077) covalent geometry : angle 0.49171 / 0.28 ( 9951) hydrogen bonds : bond 0.05598 / 5.25 ( 372) hydrogen bonds : angle 5.11561 / 6.10 ( 995) Misc. bond : bond 0.00647 / 0.32 ( 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 103 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.314 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: 19 outliers final: 17 residues processed: 98 average time/residue: 0.1457 time to fit residues: 20.4750 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 : 0.328 ------------------------------------------------------------------------------- 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 71 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 9 LYS 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: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.157749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.119469 restraints weight = 32343.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.124140 restraints weight = 17338.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.127242 restraints weight = 11231.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.129309 restraints weight = 8364.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.130450 restraints weight = 6865.423| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7078 Z= 0.167 Angle : 0.499 3.989 9951 Z= 0.287 Chirality : 0.038 0.139 1232 Planarity : 0.004 0.034 991 Dihedral : 21.571 170.200 1922 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.21 % Allowed : 26.65 % Favored : 69.14 % 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: -0.26 (0.32), residues: 694 helix: 0.94 (0.27), residues: 351 sheet: -0.63 (0.56), residues: 77 loop : -1.51 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 532 TYR 0.018 0.002 TYR K 314 PHE 0.012 0.002 PHE B 506 TRP 0.006 0.001 TRP K 302 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 7077) covalent geometry : angle 0.49886 / 0.29 ( 9951) hydrogen bonds : bond 0.05624 / 5.28 ( 372) hydrogen bonds : angle 5.08724 / 6.07 ( 995) Misc. bond : bond 0.00596 / 0.30 ( 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 103 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.441 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: K 233 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6267 (tt0) REVERT: C 140 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6846 (tt0) outliers start: 21 outliers final: 17 residues processed: 97 average time/residue: 0.1450 time to fit residues: 20.0854 Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 71 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 233 GLU 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 9 LYS 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: 0.9980 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.160777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.122406 restraints weight = 33544.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.127257 restraints weight = 17657.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.130489 restraints weight = 11336.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.132416 restraints weight = 8457.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.133735 restraints weight = 7039.004| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7078 Z= 0.138 Angle : 0.485 4.062 9951 Z= 0.277 Chirality : 0.038 0.140 1232 Planarity : 0.004 0.032 991 Dihedral : 21.545 170.903 1922 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.61 % Allowed : 26.85 % Favored : 69.54 % 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: 1.05 (0.27), residues: 351 sheet: -0.93 (0.55), residues: 82 loop : -1.32 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.018 0.002 TYR K 314 PHE 0.009 0.001 PHE B 468 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 0.00298 / 0.14 ( 7077) covalent geometry : angle 0.48547 / 0.28 ( 9951) hydrogen bonds : bond 0.05334 / 4.98 ( 372) hydrogen bonds : angle 4.98697 / 5.93 ( 995) Misc. bond : bond 0.00588 / 0.29 ( 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 104 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 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: 0.6580 (m) cc_final: 0.6341 (m) REVERT: K 233 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6225 (tt0) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.1449 time to fit residues: 20.2481 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 : 0.322 ------------------------------------------------------------------------------- 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 483 ASP 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 233 GLU 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 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 132 ASN K 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.160358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.122072 restraints weight = 33698.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.126917 restraints weight = 17752.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.130068 restraints weight = 11437.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.132073 restraints weight = 8507.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.133225 restraints weight = 7041.754| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7078 Z= 0.148 Angle : 0.492 5.116 9951 Z= 0.282 Chirality : 0.038 0.143 1232 Planarity : 0.004 0.033 991 Dihedral : 21.509 170.564 1922 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.61 % Allowed : 27.86 % Favored : 68.54 % 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: 1.02 (0.27), residues: 351 sheet: -0.92 (0.55), residues: 82 loop : -1.35 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.025 0.002 TYR K 127 PHE 0.010 0.001 PHE B 506 TRP 0.007 0.001 TRP K 302 HIS 0.010 0.002 HIS K 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7077) covalent geometry : angle 0.49165 / 0.28 ( 9951) hydrogen bonds : bond 0.05407 / 5.05 ( 372) hydrogen bonds : angle 4.97746 / 5.95 ( 995) Misc. bond : bond 0.00571 / 0.29 ( 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 : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 THR cc_start: 0.6576 (m) cc_final: 0.6333 (m) REVERT: K 233 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6202 (tt0) outliers start: 18 outliers final: 17 residues processed: 94 average time/residue: 0.1270 time to fit residues: 17.0104 Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU 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 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.158265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.120196 restraints weight = 32500.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.124921 restraints weight = 17308.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.128065 restraints weight = 11135.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.130161 restraints weight = 8245.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131280 restraints weight = 6744.226| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 7078 Z= 0.317 Angle : 0.935 59.185 9951 Z= 0.632 Chirality : 0.038 0.143 1232 Planarity : 0.004 0.033 991 Dihedral : 21.512 170.585 1922 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.41 % Allowed : 28.26 % Favored : 68.34 % 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: -0.14 (0.32), residues: 694 helix: 1.04 (0.27), residues: 351 sheet: -0.91 (0.55), residues: 82 loop : -1.35 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 84 TYR 0.020 0.002 TYR K 127 PHE 0.010 0.001 PHE B 506 TRP 0.006 0.001 TRP K 291 HIS 0.008 0.002 HIS K 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.32 ( 7077) covalent geometry : angle 0.93452 / 0.63 ( 9951) hydrogen bonds : bond 0.05404 / 5.04 ( 372) hydrogen bonds : angle 4.97403 / 5.94 ( 995) Misc. bond : bond 0.00566 / 0.28 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.88 seconds wall clock time: 44 minutes 16.09 seconds (2656.09 seconds total)