Starting phenix.real_space_refine on Fri Aug 22 19:15:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.map" model { file = "/net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sne_40624/08_2025/8sne_40624.cif" } resolution = 3.0 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= -0.001 sd= 0.062 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 1384 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 Mn 2 7.51 5 P 3 5.49 5 S 33 5.16 5 C 3883 2.51 5 N 988 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6025 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3979 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 13, 'TRANS': 474} Chain breaks: 2 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BDP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MN': 2, '3PE': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.81, per 1000 atoms: 0.30 Number of scatterers: 6025 At special positions: 0 Unit cell: (65.88, 75.6, 165.24, 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) Mn 2 24.99 S 33 16.00 P 3 15.00 O 1116 8.00 N 988 7.00 C 3883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " BDP D 2 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 390.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 45.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 3.983A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.923A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.835A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.148A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 4.874A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 354 removed outlier: 4.821A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 6.886A pdb=" N PHE A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 392 removed outlier: 4.280A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.811A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.975A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.568A pdb=" N PHE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.686A pdb=" N ARG C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.145A pdb=" N THR C 90 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 7.132A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 317 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 227 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 319 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY A 229 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 321 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N CYS A 231 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL A 323 " --> pdb=" O CYS A 231 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N ILE A 233 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TRP A 325 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.183A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.734A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.734A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.577A pdb=" N ASP C 33 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN C 32 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 52 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 23 332 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 936 1.31 - 1.43: 1779 1.43 - 1.56: 3395 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 6169 Sorted by residual: bond pdb=" C2' UDP A 601 " pdb=" C1' UDP A 601 " ideal model delta sigma weight residual 1.530 1.327 0.203 1.40e-02 5.10e+03 2.11e+02 bond pdb=" O4' UDP A 601 " pdb=" C1' UDP A 601 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.40e-02 5.10e+03 1.75e+02 bond pdb=" C4' UDP A 601 " pdb=" C3' UDP A 601 " ideal model delta sigma weight residual 1.526 1.365 0.161 1.30e-02 5.92e+03 1.54e+02 bond pdb=" C5 UDP A 601 " pdb=" C6 UDP A 601 " ideal model delta sigma weight residual 1.343 1.490 -0.147 1.60e-02 3.91e+03 8.49e+01 bond pdb=" C3' UDP A 601 " pdb=" C2' UDP A 601 " ideal model delta sigma weight residual 1.530 1.627 -0.097 1.30e-02 5.92e+03 5.62e+01 ... (remaining 6164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 8241 2.88 - 5.76: 116 5.76 - 8.65: 14 8.65 - 11.53: 1 11.53 - 14.41: 1 Bond angle restraints: 8373 Sorted by residual: angle pdb=" C2 UDP A 601 " pdb=" N3 UDP A 601 " pdb=" C4 UDP A 601 " ideal model delta sigma weight residual 126.93 120.16 6.77 1.00e+00 1.00e+00 4.59e+01 angle pdb=" O2B UDP A 601 " pdb=" PB UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 102.95 109.34 -6.39 1.00e+00 1.00e+00 4.09e+01 angle pdb=" O1B UDP A 601 " pdb=" PB UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 102.95 109.32 -6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" O5' UDP A 601 " pdb=" PA UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 104.35 110.17 -5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" N1 UDP A 601 " pdb=" C2 UDP A 601 " pdb=" N3 UDP A 601 " ideal model delta sigma weight residual 114.79 120.08 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 8368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3153 17.64 - 35.28: 395 35.28 - 52.92: 113 52.92 - 70.55: 38 70.55 - 88.19: 6 Dihedral angle restraints: 3705 sinusoidal: 1564 harmonic: 2141 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual -86.00 -20.16 -65.84 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA GLN A 172 " pdb=" C GLN A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CG ARG A 508 " pdb=" CD ARG A 508 " pdb=" NE ARG A 508 " pdb=" CZ ARG A 508 " ideal model delta sinusoidal sigma weight residual -90.00 -132.61 42.61 2 1.50e+01 4.44e-03 9.78e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 868 0.093 - 0.186: 48 0.186 - 0.278: 4 0.278 - 0.371: 1 0.371 - 0.464: 1 Chirality restraints: 922 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CBH Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CAZ Y01 A 602 " pdb=" CBF Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.55 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CBE Y01 A 602 " pdb=" CAP Y01 A 602 " pdb=" CBB Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.57 2.82 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 919 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 87 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 271 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 13 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 14 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.016 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 101 2.67 - 3.22: 5397 3.22 - 3.78: 9296 3.78 - 4.34: 12678 4.34 - 4.90: 21775 Nonbonded interactions: 49247 Sorted by model distance: nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.108 3.040 nonbonded pdb=" O2B UDP A 601 " pdb="MN MN A 605 " model vdw 2.174 2.320 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 604 " model vdw 2.215 2.320 nonbonded pdb=" O4 BDP D 2 " pdb=" O3B UDP A 601 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 46 " pdb=" OAG Y01 A 602 " model vdw 2.299 3.040 ... (remaining 49242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.020 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.008 0.203 6172 Z= 0.484 Angle : 0.741 14.409 8380 Z= 0.380 Chirality : 0.049 0.464 922 Planarity : 0.004 0.055 1027 Dihedral : 17.690 88.192 2335 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 0.63 % Allowed : 24.09 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.32), residues: 725 helix: 1.32 (0.30), residues: 312 sheet: 0.22 (0.44), residues: 146 loop : -1.50 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.016 0.001 TYR A 414 PHE 0.014 0.001 PHE A 450 TRP 0.012 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 6169) covalent geometry : angle 0.74056 ( 8373) SS BOND : bond 0.00379 ( 2) SS BOND : angle 1.53782 ( 4) hydrogen bonds : bond 0.12315 ( 320) hydrogen bonds : angle 5.62656 ( 915) link_BETA1-3 : bond 0.00349 ( 1) link_BETA1-3 : angle 0.91520 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8746 (ppp) cc_final: 0.8200 (ppp) REVERT: C 38 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7798 (ttm170) outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 0.5901 time to fit residues: 53.2264 Evaluate side-chains 80 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134998 restraints weight = 6680.242| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.96 r_work: 0.3152 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6172 Z= 0.138 Angle : 0.512 7.748 8380 Z= 0.268 Chirality : 0.042 0.170 922 Planarity : 0.004 0.054 1027 Dihedral : 9.285 83.483 1017 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 3.80 % Allowed : 23.30 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.32), residues: 725 helix: 1.57 (0.30), residues: 315 sheet: 0.36 (0.44), residues: 142 loop : -1.49 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.016 0.001 TYR A 414 PHE 0.013 0.001 PHE A 450 TRP 0.012 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6169) covalent geometry : angle 0.51013 ( 8373) SS BOND : bond 0.00153 ( 2) SS BOND : angle 1.62585 ( 4) hydrogen bonds : bond 0.04083 ( 320) hydrogen bonds : angle 4.41711 ( 915) link_BETA1-3 : bond 0.00128 ( 1) link_BETA1-3 : angle 1.15761 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7362 (mpt180) REVERT: C 38 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7609 (ttm170) outliers start: 24 outliers final: 10 residues processed: 95 average time/residue: 0.5106 time to fit residues: 51.0757 Evaluate side-chains 86 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141420 restraints weight = 6516.856| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.85 r_work: 0.3227 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6172 Z= 0.097 Angle : 0.469 8.424 8380 Z= 0.246 Chirality : 0.041 0.148 922 Planarity : 0.004 0.053 1027 Dihedral : 8.646 87.449 1017 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 3.65 % Allowed : 23.77 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.32), residues: 725 helix: 1.84 (0.30), residues: 315 sheet: 0.17 (0.43), residues: 155 loop : -1.35 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 334 TYR 0.013 0.001 TYR A 414 PHE 0.011 0.001 PHE A 450 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 6169) covalent geometry : angle 0.46845 ( 8373) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.29924 ( 4) hydrogen bonds : bond 0.03523 ( 320) hydrogen bonds : angle 4.11461 ( 915) link_BETA1-3 : bond 0.00436 ( 1) link_BETA1-3 : angle 0.71769 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7231 (mp) REVERT: C 23 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7035 (tp-100) REVERT: C 38 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7482 (ttm170) outliers start: 23 outliers final: 3 residues processed: 95 average time/residue: 0.5425 time to fit residues: 53.9330 Evaluate side-chains 78 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139182 restraints weight = 6561.146| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.90 r_work: 0.3145 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6172 Z= 0.142 Angle : 0.510 9.882 8380 Z= 0.265 Chirality : 0.042 0.147 922 Planarity : 0.004 0.053 1027 Dihedral : 8.555 89.146 1016 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 5.39 % Allowed : 22.35 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.32), residues: 725 helix: 1.72 (0.30), residues: 314 sheet: 0.20 (0.43), residues: 153 loop : -1.37 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.016 0.001 TYR A 414 PHE 0.011 0.001 PHE A 450 TRP 0.011 0.001 TRP A 246 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6169) covalent geometry : angle 0.50931 ( 8373) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.96053 ( 4) hydrogen bonds : bond 0.03937 ( 320) hydrogen bonds : angle 4.13625 ( 915) link_BETA1-3 : bond 0.00453 ( 1) link_BETA1-3 : angle 0.79004 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7291 (mp) REVERT: A 139 ASN cc_start: 0.7699 (m-40) cc_final: 0.7481 (m-40) REVERT: A 166 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (mtpt) REVERT: C 23 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7004 (tp40) REVERT: C 38 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7485 (ttm170) REVERT: C 104 ARG cc_start: 0.7569 (mtm110) cc_final: 0.6833 (mmm160) outliers start: 34 outliers final: 10 residues processed: 99 average time/residue: 0.4881 time to fit residues: 51.1050 Evaluate side-chains 87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.178889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136614 restraints weight = 6724.929| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.94 r_work: 0.3230 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6172 Z= 0.112 Angle : 0.500 13.227 8380 Z= 0.256 Chirality : 0.041 0.143 922 Planarity : 0.004 0.052 1027 Dihedral : 8.325 89.040 1016 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 4.28 % Allowed : 23.61 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.32), residues: 725 helix: 1.79 (0.30), residues: 315 sheet: 0.26 (0.42), residues: 152 loop : -1.32 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.014 0.001 TYR A 414 PHE 0.009 0.001 PHE A 450 TRP 0.010 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6169) covalent geometry : angle 0.49934 ( 8373) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.77716 ( 4) hydrogen bonds : bond 0.03622 ( 320) hydrogen bonds : angle 4.02532 ( 915) link_BETA1-3 : bond 0.00397 ( 1) link_BETA1-3 : angle 0.79028 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 139 ASN cc_start: 0.7601 (t0) cc_final: 0.7359 (m-40) REVERT: A 166 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8582 (mtpt) REVERT: A 284 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6379 (ttpt) REVERT: C 23 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7012 (tp40) REVERT: C 38 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7303 (ttm170) REVERT: C 104 ARG cc_start: 0.7539 (mtm110) cc_final: 0.6816 (mmm160) outliers start: 27 outliers final: 9 residues processed: 95 average time/residue: 0.5353 time to fit residues: 53.6061 Evaluate side-chains 87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 86 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141030 restraints weight = 6656.392| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.96 r_work: 0.3262 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6172 Z= 0.088 Angle : 0.484 12.659 8380 Z= 0.245 Chirality : 0.040 0.140 922 Planarity : 0.004 0.052 1027 Dihedral : 7.890 86.089 1016 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 3.01 % Allowed : 25.83 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.32), residues: 725 helix: 2.03 (0.30), residues: 315 sheet: 0.36 (0.43), residues: 146 loop : -1.31 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 334 TYR 0.013 0.001 TYR B 94 PHE 0.010 0.001 PHE C 67 TRP 0.007 0.000 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 6169) covalent geometry : angle 0.48356 ( 8373) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.71640 ( 4) hydrogen bonds : bond 0.03177 ( 320) hydrogen bonds : angle 3.88851 ( 915) link_BETA1-3 : bond 0.00370 ( 1) link_BETA1-3 : angle 0.88361 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7248 (mp) REVERT: A 49 PHE cc_start: 0.7881 (t80) cc_final: 0.7421 (t80) REVERT: A 139 ASN cc_start: 0.7498 (t0) cc_final: 0.7227 (m-40) REVERT: A 284 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6298 (ttpt) REVERT: C 38 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7364 (ttm170) outliers start: 19 outliers final: 6 residues processed: 91 average time/residue: 0.5065 time to fit residues: 48.4723 Evaluate side-chains 83 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 3 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 52 optimal weight: 0.0670 chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141201 restraints weight = 6698.472| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3269 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6172 Z= 0.092 Angle : 0.485 12.547 8380 Z= 0.246 Chirality : 0.040 0.139 922 Planarity : 0.004 0.051 1027 Dihedral : 7.598 85.251 1016 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 3.33 % Allowed : 27.10 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.32), residues: 725 helix: 2.08 (0.30), residues: 315 sheet: 0.42 (0.42), residues: 146 loop : -1.23 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 334 TYR 0.013 0.001 TYR A 414 PHE 0.009 0.001 PHE A 49 TRP 0.008 0.000 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6169) covalent geometry : angle 0.48431 ( 8373) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.65387 ( 4) hydrogen bonds : bond 0.03158 ( 320) hydrogen bonds : angle 3.84828 ( 915) link_BETA1-3 : bond 0.00284 ( 1) link_BETA1-3 : angle 0.83258 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7094 (mp) REVERT: A 49 PHE cc_start: 0.7859 (t80) cc_final: 0.7366 (t80) REVERT: A 139 ASN cc_start: 0.7537 (t0) cc_final: 0.7236 (m-40) REVERT: A 190 MET cc_start: 0.8444 (ppp) cc_final: 0.7935 (ppp) REVERT: A 284 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6497 (ttpt) REVERT: A 349 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 71 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7114 (tpp80) REVERT: C 104 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6777 (mmm160) outliers start: 21 outliers final: 10 residues processed: 92 average time/residue: 0.5176 time to fit residues: 49.8663 Evaluate side-chains 90 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.181500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139032 restraints weight = 6650.669| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3239 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6172 Z= 0.107 Angle : 0.497 12.362 8380 Z= 0.253 Chirality : 0.041 0.142 922 Planarity : 0.004 0.051 1027 Dihedral : 7.548 85.433 1016 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 3.33 % Allowed : 27.26 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.32), residues: 725 helix: 2.03 (0.30), residues: 314 sheet: 0.39 (0.43), residues: 148 loop : -1.24 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.014 0.001 TYR A 414 PHE 0.009 0.001 PHE A 450 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6169) covalent geometry : angle 0.49640 ( 8373) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.75608 ( 4) hydrogen bonds : bond 0.03375 ( 320) hydrogen bonds : angle 3.89300 ( 915) link_BETA1-3 : bond 0.00341 ( 1) link_BETA1-3 : angle 0.82246 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7062 (mp) REVERT: A 49 PHE cc_start: 0.7779 (t80) cc_final: 0.7281 (t80) REVERT: A 139 ASN cc_start: 0.7665 (t0) cc_final: 0.7337 (m-40) REVERT: A 166 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8375 (mtpp) REVERT: A 190 MET cc_start: 0.8633 (ppp) cc_final: 0.8063 (ppp) REVERT: A 284 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6508 (ttpt) REVERT: A 349 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 23 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6964 (tp40) REVERT: C 71 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7104 (tpp80) REVERT: C 104 ARG cc_start: 0.7475 (mtm110) cc_final: 0.6759 (mmm160) outliers start: 21 outliers final: 8 residues processed: 92 average time/residue: 0.5459 time to fit residues: 52.6696 Evaluate side-chains 88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132690 restraints weight = 6675.938| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.90 r_work: 0.3157 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6172 Z= 0.147 Angle : 0.535 12.511 8380 Z= 0.275 Chirality : 0.043 0.145 922 Planarity : 0.004 0.051 1027 Dihedral : 7.641 86.275 1016 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 2.54 % Allowed : 28.05 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.32), residues: 725 helix: 1.82 (0.30), residues: 314 sheet: 0.49 (0.44), residues: 143 loop : -1.33 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 334 TYR 0.016 0.001 TYR A 414 PHE 0.010 0.001 PHE A 450 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6169) covalent geometry : angle 0.53431 ( 8373) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.98393 ( 4) hydrogen bonds : bond 0.03888 ( 320) hydrogen bonds : angle 4.02705 ( 915) link_BETA1-3 : bond 0.00340 ( 1) link_BETA1-3 : angle 0.82629 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.194 Fit side-chains REVERT: A 43 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7058 (mp) REVERT: A 49 PHE cc_start: 0.7797 (t80) cc_final: 0.7288 (t80) REVERT: A 139 ASN cc_start: 0.7747 (t0) cc_final: 0.7429 (m-40) REVERT: A 166 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: A 190 MET cc_start: 0.8673 (ppp) cc_final: 0.8035 (ppp) REVERT: A 284 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6437 (ttpt) REVERT: C 23 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6727 (tp40) REVERT: C 71 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7061 (tpp80) REVERT: C 104 ARG cc_start: 0.7521 (mtm110) cc_final: 0.6809 (mmm160) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.5278 time to fit residues: 48.7361 Evaluate side-chains 91 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.179998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137318 restraints weight = 6582.414| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.94 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6172 Z= 0.110 Angle : 0.510 12.384 8380 Z= 0.261 Chirality : 0.041 0.147 922 Planarity : 0.004 0.050 1027 Dihedral : 7.442 83.860 1016 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 2.85 % Allowed : 27.73 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.32), residues: 725 helix: 1.89 (0.30), residues: 315 sheet: 0.59 (0.44), residues: 142 loop : -1.30 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 75 TYR 0.014 0.001 TYR A 414 PHE 0.009 0.001 PHE A 450 TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6169) covalent geometry : angle 0.50934 ( 8373) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.80556 ( 4) hydrogen bonds : bond 0.03509 ( 320) hydrogen bonds : angle 3.95092 ( 915) link_BETA1-3 : bond 0.00386 ( 1) link_BETA1-3 : angle 0.84978 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.248 Fit side-chains REVERT: A 43 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7145 (mp) REVERT: A 49 PHE cc_start: 0.7791 (t80) cc_final: 0.7291 (t80) REVERT: A 139 ASN cc_start: 0.7618 (t0) cc_final: 0.7293 (m-40) REVERT: A 166 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: A 190 MET cc_start: 0.8664 (ppp) cc_final: 0.8036 (ppp) REVERT: A 284 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6379 (ttpt) REVERT: A 349 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8120 (mm-30) outliers start: 18 outliers final: 8 residues processed: 87 average time/residue: 0.4689 time to fit residues: 43.2404 Evaluate side-chains 83 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136955 restraints weight = 6578.349| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.92 r_work: 0.3209 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6172 Z= 0.116 Angle : 0.514 12.405 8380 Z= 0.262 Chirality : 0.041 0.144 922 Planarity : 0.004 0.062 1027 Dihedral : 7.368 82.641 1016 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 2.85 % Allowed : 27.89 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.32), residues: 725 helix: 1.88 (0.30), residues: 314 sheet: 0.48 (0.43), residues: 144 loop : -1.27 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 75 TYR 0.015 0.001 TYR A 414 PHE 0.009 0.001 PHE A 450 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6169) covalent geometry : angle 0.51380 ( 8373) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.86607 ( 4) hydrogen bonds : bond 0.03569 ( 320) hydrogen bonds : angle 3.95995 ( 915) link_BETA1-3 : bond 0.00379 ( 1) link_BETA1-3 : angle 0.82305 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.02 seconds wall clock time: 39 minutes 34.85 seconds (2374.85 seconds total)