Starting phenix.real_space_refine on Sun Aug 24 07:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443.map" model { file = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up5_42443/08_2025/8up5_42443_neut.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6767 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 73 5.49 5 S 22 5.16 5 C 4076 2.51 5 N 1180 2.21 5 O 1459 1.98 5 H 5818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.89, per 1000 atoms: 0.15 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: 1.02 Conformation dependent library (CDL) restraints added in 241.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 54.6% alpha, 13.9% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'B' and resid 369 through 394 removed outlier: 4.426A pdb=" N LYS B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.475A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.751A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.928A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.542A pdb=" N VAL B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 3.720A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'K' and resid 43 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 153 through 165 Processing helix chain 'K' and resid 171 through 182 removed outlier: 3.586A pdb=" N LYS K 181 " --> pdb=" O GLU K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 212 removed outlier: 4.333A pdb=" N LEU K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 271 Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.306A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 3.996A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.940A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.651A pdb=" N VAL C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.272A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 109 through 112 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'P' and resid 16 through 33 removed outlier: 3.925A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 80 removed outlier: 3.796A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 361 removed outlier: 3.816A pdb=" N ASP B 403 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 removed outlier: 3.523A pdb=" N LYS B 419 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AA4, first strand: chain 'K' and resid 23 through 31 removed outlier: 5.765A pdb=" N VAL K 24 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR K 19 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE K 2 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA K 72 " --> pdb=" O ILE K 2 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU K 4 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER K 74 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU K 6 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLY K 76 " --> pdb=" O LEU K 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 142 through 148 removed outlier: 4.934A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL K 139 " --> pdb=" O TYR K 143 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL K 145 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA K 137 " --> pdb=" O VAL K 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY K 147 " --> pdb=" O VAL K 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.102A pdb=" N GLY C 84 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 13 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 8 through 13 321 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.36 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.070 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 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= 0.501 Angle : 0.713 11.452 9951 Z= 0.452 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 aren 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 covalent geometry : bond 0.00377 ( 7077) covalent geometry : angle 0.71348 ( 9951) hydrogen bonds : bond 0.14562 ( 372) hydrogen bonds : angle 6.72820 ( 995) Misc. bond : bond 0.37800 ( 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 : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.1869 time to fit residues: 21.7723 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 : 0.315 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4534 r_free = 0.4534 target = 0.159213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.120930 restraints weight = 32364.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.125721 restraints weight = 17246.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.128908 restraints weight = 11089.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.130966 restraints weight = 8204.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.132052 restraints weight = 6734.065| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7078 Z= 0.184 Angle : 0.541 3.871 9951 Z= 0.300 Chirality : 0.039 0.148 1232 Planarity : 0.004 0.038 991 Dihedral : 21.647 168.680 1924 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.61 % Allowed : 26.25 % Favored : 71.14 % 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 aren not related in a simple way. whole: 0.11 (0.32), residues: 694 helix: 1.23 (0.27), residues: 351 sheet: -0.23 (0.57), residues: 77 loop : -1.41 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 84 TYR 0.022 0.002 TYR K 314 PHE 0.014 0.001 PHE B 506 TRP 0.006 0.001 TRP K 291 HIS 0.007 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7077) covalent geometry : angle 0.54087 ( 9951) hydrogen bonds : bond 0.05860 ( 372) hydrogen bonds : angle 5.46443 ( 995) Misc. bond : bond 0.00538 ( 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 : 0.387 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: 11 residues processed: 96 average time/residue: 0.1693 time to fit residues: 22.1232 Evaluate side-chains 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 87 CYS Chi-restraints excluded: chain C residue 121 LEU 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: 10.0000 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.159283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120742 restraints weight = 32437.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.125642 restraints weight = 17201.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.128876 restraints weight = 11032.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.130974 restraints weight = 8147.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.131834 restraints weight = 6680.070| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7078 Z= 0.146 Angle : 0.497 3.687 9951 Z= 0.277 Chirality : 0.038 0.139 1232 Planarity : 0.004 0.032 991 Dihedral : 21.528 169.619 1922 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.41 % Allowed : 25.85 % 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 aren not related in a simple way. whole: 0.20 (0.32), residues: 694 helix: 1.33 (0.28), residues: 351 sheet: -0.36 (0.57), residues: 77 loop : -1.34 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.017 0.002 TYR K 314 PHE 0.016 0.001 PHE B 468 TRP 0.006 0.001 TRP K 302 HIS 0.006 0.001 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7077) covalent geometry : angle 0.49680 ( 9951) hydrogen bonds : bond 0.05086 ( 372) hydrogen bonds : angle 5.06248 ( 995) Misc. bond : bond 0.00455 ( 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 106 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 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: K 135 VAL cc_start: 0.6950 (OUTLIER) cc_final: 0.6722 (p) REVERT: C 140 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7001 (tt0) outliers start: 17 outliers final: 10 residues processed: 101 average time/residue: 0.1688 time to fit residues: 23.2499 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 : 0.311 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 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: 2.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.156479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.118120 restraints weight = 32695.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.122735 restraints weight = 17620.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125855 restraints weight = 11478.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.127902 restraints weight = 8547.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.129079 restraints weight = 7041.320| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7078 Z= 0.205 Angle : 0.542 3.780 9951 Z= 0.303 Chirality : 0.039 0.144 1232 Planarity : 0.004 0.037 991 Dihedral : 21.580 169.954 1922 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.41 % Allowed : 26.45 % 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 aren not related in a simple way. whole: -0.34 (0.31), residues: 694 helix: 0.88 (0.27), residues: 351 sheet: -0.55 (0.56), residues: 77 loop : -1.61 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 38 TYR 0.019 0.002 TYR K 314 PHE 0.014 0.002 PHE B 506 TRP 0.006 0.001 TRP K 302 HIS 0.004 0.002 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7077) covalent geometry : angle 0.54226 ( 9951) hydrogen bonds : bond 0.05768 ( 372) hydrogen bonds : angle 5.21571 ( 995) Misc. bond : bond 0.00582 ( 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 108 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.320 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 106 HIS cc_start: 0.6445 (t70) cc_final: 0.6218 (t-170) REVERT: K 135 VAL cc_start: 0.7084 (OUTLIER) cc_final: 0.6842 (p) REVERT: C 140 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7097 (tt0) outliers start: 22 outliers final: 15 residues processed: 101 average time/residue: 0.1688 time to fit residues: 23.4526 Evaluate side-chains 97 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 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 319 VAL Chi-restraints excluded: chain C residue 87 CYS 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 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.122099 restraints weight = 33752.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126993 restraints weight = 17889.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.130196 restraints weight = 11467.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.132172 restraints weight = 8542.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.133492 restraints weight = 7073.385| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7078 Z= 0.153 Angle : 0.509 3.847 9951 Z= 0.282 Chirality : 0.038 0.139 1232 Planarity : 0.004 0.033 991 Dihedral : 21.546 171.396 1922 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.21 % Allowed : 26.45 % 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 aren not related in a simple way. whole: -0.17 (0.32), residues: 694 helix: 0.98 (0.27), residues: 353 sheet: -0.69 (0.55), residues: 77 loop : -1.41 (0.38), residues: 264 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 0.010 0.001 PHE B 468 TRP 0.006 0.001 TRP K 302 HIS 0.006 0.002 HIS K 110 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7077) covalent geometry : angle 0.50865 ( 9951) hydrogen bonds : bond 0.05094 ( 372) hydrogen bonds : angle 4.99615 ( 995) Misc. bond : bond 0.00602 ( 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 108 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 106 HIS cc_start: 0.6296 (t70) cc_final: 0.6037 (t-170) REVERT: K 135 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6814 (p) REVERT: K 233 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6059 (tt0) REVERT: C 140 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6886 (tt0) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.1190 time to fit residues: 17.7686 Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 507 LEU 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 135 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 292 LEU Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.156528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118709 restraints weight = 32732.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.123300 restraints weight = 17547.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126382 restraints weight = 11374.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.128335 restraints weight = 8481.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.129445 restraints weight = 6995.672| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7078 Z= 0.179 Angle : 0.525 3.870 9951 Z= 0.292 Chirality : 0.038 0.142 1232 Planarity : 0.004 0.036 991 Dihedral : 21.545 170.595 1922 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.61 % Allowed : 26.65 % Favored : 68.74 % 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 aren not related in a simple way. whole: -0.35 (0.31), residues: 694 helix: 0.84 (0.27), residues: 353 sheet: -0.71 (0.55), residues: 77 loop : -1.53 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 532 TYR 0.019 0.002 TYR K 314 PHE 0.012 0.002 PHE B 468 TRP 0.006 0.001 TRP K 302 HIS 0.005 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7077) covalent geometry : angle 0.52483 ( 9951) hydrogen bonds : bond 0.05497 ( 372) hydrogen bonds : angle 5.06991 ( 995) Misc. bond : bond 0.00645 ( 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 109 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.321 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 135 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6768 (p) REVERT: K 233 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6157 (tt0) REVERT: C 60 MET cc_start: 0.4983 (ttm) cc_final: 0.4657 (tmm) REVERT: C 140 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7640 (tm-30) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.1448 time to fit residues: 20.6288 Evaluate side-chains 103 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 507 LEU 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 135 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 262 MET Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 292 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.158702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.120911 restraints weight = 31999.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125700 restraints weight = 16565.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.128940 restraints weight = 10444.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130999 restraints weight = 7641.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.132137 restraints weight = 6226.920| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7078 Z= 0.125 Angle : 0.493 3.883 9951 Z= 0.272 Chirality : 0.038 0.145 1232 Planarity : 0.004 0.030 991 Dihedral : 21.481 171.617 1922 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.21 % Allowed : 27.45 % Favored : 68.34 % 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 aren not related in a simple way. whole: 0.07 (0.32), residues: 694 helix: 1.15 (0.28), residues: 353 sheet: -0.73 (0.54), residues: 77 loop : -1.20 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.020 0.002 TYR K 127 PHE 0.011 0.001 PHE C 27 TRP 0.007 0.001 TRP K 302 HIS 0.008 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7077) covalent geometry : angle 0.49258 ( 9951) hydrogen bonds : bond 0.04838 ( 372) hydrogen bonds : angle 4.86819 ( 995) Misc. bond : bond 0.00623 ( 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 107 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 464 TYR cc_start: 0.5266 (m-80) cc_final: 0.5057 (m-10) REVERT: K 135 VAL cc_start: 0.7003 (OUTLIER) cc_final: 0.6729 (p) REVERT: C 60 MET cc_start: 0.4908 (ttm) cc_final: 0.4614 (tmm) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.1479 time to fit residues: 21.2228 Evaluate side-chains 97 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 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 292 LEU 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 P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4513 r_free = 0.4513 target = 0.157372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.119701 restraints weight = 32305.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.124216 restraints weight = 17564.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.127156 restraints weight = 11451.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.129117 restraints weight = 8572.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.130257 restraints weight = 7059.097| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7078 Z= 0.161 Angle : 0.512 3.913 9951 Z= 0.284 Chirality : 0.038 0.143 1232 Planarity : 0.004 0.032 991 Dihedral : 21.470 170.660 1922 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.41 % Allowed : 27.05 % 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 aren not related in a simple way. whole: -0.07 (0.32), residues: 694 helix: 1.02 (0.27), residues: 354 sheet: -0.75 (0.55), residues: 77 loop : -1.26 (0.38), residues: 263 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 0.013 0.002 PHE B 468 TRP 0.006 0.001 TRP K 291 HIS 0.009 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7077) covalent geometry : angle 0.51245 ( 9951) hydrogen bonds : bond 0.05292 ( 372) hydrogen bonds : angle 4.94301 ( 995) Misc. bond : bond 0.00628 ( 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 105 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 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: K 233 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6171 (tt0) REVERT: C 60 MET cc_start: 0.4990 (ttm) cc_final: 0.4701 (tmm) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1390 time to fit residues: 19.3168 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 483 ASP Chi-restraints excluded: chain B residue 507 LEU 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 273 ASP Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4530 r_free = 0.4530 target = 0.158545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.120980 restraints weight = 31963.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125665 restraints weight = 16753.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.128765 restraints weight = 10661.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.130713 restraints weight = 7834.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.132035 restraints weight = 6439.059| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7078 Z= 0.129 Angle : 0.495 3.915 9951 Z= 0.273 Chirality : 0.037 0.142 1232 Planarity : 0.004 0.032 991 Dihedral : 21.427 171.647 1922 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.81 % Allowed : 28.26 % Favored : 67.94 % 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 aren not related in a simple way. whole: 0.15 (0.32), residues: 694 helix: 1.16 (0.28), residues: 354 sheet: -0.71 (0.55), residues: 77 loop : -1.06 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.020 0.002 TYR P 36 PHE 0.009 0.001 PHE B 468 TRP 0.007 0.001 TRP K 302 HIS 0.007 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7077) covalent geometry : angle 0.49500 ( 9951) hydrogen bonds : bond 0.04880 ( 372) hydrogen bonds : angle 4.83052 ( 995) Misc. bond : bond 0.00620 ( 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 108 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.264 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: 0.6486 (OUTLIER) cc_final: 0.6149 (tt0) REVERT: K 279 LYS cc_start: 0.7871 (tptp) cc_final: 0.7610 (tptm) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.1274 time to fit residues: 18.2832 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 : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 507 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 233 GLU Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL 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: 2.9990 chunk 11 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121378 restraints weight = 32480.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126254 restraints weight = 17141.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.129336 restraints weight = 10926.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.130990 restraints weight = 8090.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.132610 restraints weight = 6750.298| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7078 Z= 0.115 Angle : 0.492 4.151 9951 Z= 0.270 Chirality : 0.037 0.141 1232 Planarity : 0.003 0.035 991 Dihedral : 21.392 171.709 1922 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.61 % Allowed : 28.66 % Favored : 67.74 % 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 aren not related in a simple way. whole: 0.34 (0.33), residues: 694 helix: 1.28 (0.28), residues: 354 sheet: -0.56 (0.55), residues: 78 loop : -0.94 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.020 0.002 TYR K 127 PHE 0.010 0.001 PHE B 468 TRP 0.007 0.001 TRP K 291 HIS 0.006 0.001 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7077) covalent geometry : angle 0.49166 ( 9951) hydrogen bonds : bond 0.04835 ( 372) hydrogen bonds : angle 4.76918 ( 995) Misc. bond : bond 0.00617 ( 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 106 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.247 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 233 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6070 (tt0) REVERT: K 279 LYS cc_start: 0.7891 (tptp) cc_final: 0.7632 (tptm) outliers start: 18 outliers final: 17 residues processed: 100 average time/residue: 0.1466 time to fit residues: 20.3536 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 : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 483 ASP Chi-restraints excluded: chain B residue 507 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 233 GLU Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.158368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.120213 restraints weight = 32573.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.124967 restraints weight = 17307.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.128069 restraints weight = 11098.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.130132 restraints weight = 8203.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.131160 restraints weight = 6719.936| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7078 Z= 0.140 Angle : 0.502 4.214 9951 Z= 0.278 Chirality : 0.037 0.139 1232 Planarity : 0.004 0.033 991 Dihedral : 21.369 171.481 1922 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.21 % Allowed : 27.86 % Favored : 67.94 % 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 aren not related in a simple way. whole: 0.28 (0.33), residues: 694 helix: 1.22 (0.28), residues: 354 sheet: -0.57 (0.53), residues: 87 loop : -0.96 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.019 0.002 TYR P 36 PHE 0.012 0.001 PHE B 468 TRP 0.006 0.001 TRP K 302 HIS 0.005 0.002 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7077) covalent geometry : angle 0.50234 ( 9951) hydrogen bonds : bond 0.05111 ( 372) hydrogen bonds : angle 4.82520 ( 995) Misc. bond : bond 0.00588 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2577.55 seconds wall clock time: 44 minutes 34.40 seconds (2674.40 seconds total)