Starting phenix.real_space_refine on Fri Oct 10 13:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smn_40594/10_2025/8smn_40594.map" } resolution = 3.2 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 3971 2.51 5 N 981 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6138 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4286 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain breaks: 2 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 119 Unusual residues: {'BDP': 4, 'NAG': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.24 Number of scatterers: 6138 At special positions: 0 Unit cell: (65.88, 78.84, 139.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1138 8.00 N 981 7.00 C 3971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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 B 1 " - " BDP B 2 " " NAG B 3 " - " BDP B 4 " " NAG B 5 " - " BDP B 6 " " NAG B 7 " - " BDP B 8 " BETA1-4 " BDP B 2 " - " NAG B 3 " " BDP B 4 " - " NAG B 5 " " BDP B 6 " - " NAG B 7 " " BDP B 8 " - " NAG B 9 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 349.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 46.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 49 removed outlier: 3.544A pdb=" N GLU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 90 Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.802A pdb=" N LYS A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.032A pdb=" N MET A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.758A pdb=" N GLY A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 4.570A pdb=" N ASN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.901A pdb=" N PHE A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 5.068A pdb=" N GLU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 373 through 394 removed outlier: 4.231A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 401 through 427 removed outlier: 4.095A pdb=" N THR A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.561A pdb=" N VAL A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.002A pdb=" N MET A 461 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.523A pdb=" N TYR A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 529 removed outlier: 3.741A pdb=" N LEU A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 568 removed outlier: 3.980A pdb=" N TYR A 546 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.934A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.835A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 removed outlier: 7.027A pdb=" N LEU A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.493A pdb=" N GLY A 161 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET A 212 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 163 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 100 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 134 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 102 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 136 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 104 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 105 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 313 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 264 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TYR A 263 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 10.776A pdb=" N TYR A 358 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 10.874A pdb=" N ALA A 265 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N HIS A 360 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N GLY A 267 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER A 362 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.831A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.718A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.606A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA L 33 " --> pdb=" O SER L 92 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 921 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: 0.80 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1838 1.34 - 1.46: 1626 1.46 - 1.58: 2759 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 6300 Sorted by residual: bond pdb=" C3 BDP B 8 " pdb=" O3 BDP B 8 " ideal model delta sigma weight residual 1.411 1.516 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C3 BDP B 2 " pdb=" O3 BDP B 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3 BDP B 6 " pdb=" O3 BDP B 6 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C3 BDP B 4 " pdb=" O3 BDP B 4 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 BDP B 2 " pdb=" O5 BDP B 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 6295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8360 1.71 - 3.42: 151 3.42 - 5.13: 23 5.13 - 6.84: 10 6.84 - 8.55: 4 Bond angle restraints: 8548 Sorted by residual: angle pdb=" CA GLN A 529 " pdb=" CB GLN A 529 " pdb=" CG GLN A 529 " ideal model delta sigma weight residual 114.10 122.65 -8.55 2.00e+00 2.50e-01 1.83e+01 angle pdb=" C GLN A 529 " pdb=" CA GLN A 529 " pdb=" CB GLN A 529 " ideal model delta sigma weight residual 111.68 117.44 -5.76 1.68e+00 3.54e-01 1.17e+01 angle pdb=" C TYR A 372 " pdb=" N LEU A 373 " pdb=" CA LEU A 373 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.04e+00 angle pdb=" O6A BDP B 4 " pdb=" C6 BDP B 4 " pdb=" O6B BDP B 4 " ideal model delta sigma weight residual 127.00 119.95 7.05 3.00e+00 1.11e-01 5.53e+00 angle pdb=" C SER H 56 " pdb=" N SER H 57 " pdb=" CA SER H 57 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.51e+00 ... (remaining 8543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3234 17.80 - 35.60: 396 35.60 - 53.40: 130 53.40 - 71.21: 13 71.21 - 89.01: 12 Dihedral angle restraints: 3785 sinusoidal: 1591 harmonic: 2194 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 147.72 -54.72 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA ARG A 374 " pdb=" C ARG A 374 " pdb=" N TRP A 375 " pdb=" CA TRP A 375 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual -86.00 -115.26 29.26 1 1.00e+01 1.00e-02 1.23e+01 ... (remaining 3782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 567 0.025 - 0.050: 219 0.050 - 0.076: 100 0.076 - 0.101: 47 0.101 - 0.126: 22 Chirality restraints: 955 Sorted by residual: chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PHE A 323 " pdb=" N PHE A 323 " pdb=" C PHE A 323 " pdb=" CB PHE A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 952 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 373 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C LEU A 373 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 373 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 374 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA H 43 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO H 44 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 529 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C GLN A 529 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 529 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 530 " 0.011 2.00e-02 2.50e+03 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1092 2.77 - 3.30: 5442 3.30 - 3.84: 10216 3.84 - 4.37: 11888 4.37 - 4.90: 21424 Nonbonded interactions: 50062 Sorted by model distance: nonbonded pdb=" ND2 ASN A 140 " pdb=" O TRP A 165 " model vdw 2.239 3.120 nonbonded pdb=" O MET A 469 " pdb=" OG1 THR A 473 " model vdw 2.299 3.040 nonbonded pdb=" O SER L 31 " pdb=" OG SER L 31 " model vdw 2.319 3.040 nonbonded pdb=" O TYR A 263 " pdb=" NH1 ARG A 316 " model vdw 2.338 3.120 nonbonded pdb=" NH1 ARG A 219 " pdb=" O TYR A 328 " model vdw 2.339 3.120 ... (remaining 50057 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.040 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 6310 Z= 0.266 Angle : 0.612 8.548 8576 Z= 0.305 Chirality : 0.039 0.126 955 Planarity : 0.004 0.047 1036 Dihedral : 17.259 89.008 2383 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.15 % Allowed : 25.34 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.31), residues: 739 helix: 2.12 (0.29), residues: 329 sheet: -0.03 (0.40), residues: 177 loop : -1.32 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.010 0.001 TYR A 451 PHE 0.020 0.001 PHE A 323 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 6300) covalent geometry : angle 0.60591 ( 8548) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.51860 ( 4) hydrogen bonds : bond 0.13261 ( 327) hydrogen bonds : angle 5.42812 ( 921) link_BETA1-3 : bond 0.00264 ( 4) link_BETA1-3 : angle 1.73265 ( 12) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 1.69421 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.247 Fit side-chains REVERT: A 112 GLU cc_start: 0.7500 (tp30) cc_final: 0.6789 (tt0) REVERT: A 329 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7910 (mmt-90) REVERT: A 504 MET cc_start: 0.7782 (tpt) cc_final: 0.7362 (tpt) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.0952 time to fit residues: 12.1787 Evaluate side-chains 96 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102838 restraints weight = 7014.129| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.70 r_work: 0.2894 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6310 Z= 0.139 Angle : 0.526 5.439 8576 Z= 0.270 Chirality : 0.040 0.132 955 Planarity : 0.004 0.035 1036 Dihedral : 8.289 88.051 1022 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.75 % Allowed : 22.60 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.31), residues: 739 helix: 2.19 (0.29), residues: 330 sheet: 0.22 (0.40), residues: 183 loop : -1.24 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.012 0.001 TYR A 451 PHE 0.021 0.001 PHE A 323 TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6300) covalent geometry : angle 0.51873 ( 8548) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.20287 ( 4) hydrogen bonds : bond 0.04151 ( 327) hydrogen bonds : angle 4.22684 ( 921) link_BETA1-3 : bond 0.00268 ( 4) link_BETA1-3 : angle 1.69268 ( 12) link_BETA1-4 : bond 0.00479 ( 4) link_BETA1-4 : angle 1.74091 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.246 Fit side-chains REVERT: A 318 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7694 (p0) REVERT: A 336 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.4667 (t80) REVERT: A 461 MET cc_start: 0.8840 (mmm) cc_final: 0.8502 (mmm) REVERT: H 68 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8400 (ttpt) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.0894 time to fit residues: 13.4516 Evaluate side-chains 112 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.127623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.104631 restraints weight = 6912.613| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.61 r_work: 0.2893 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6310 Z= 0.145 Angle : 0.516 5.347 8576 Z= 0.265 Chirality : 0.040 0.135 955 Planarity : 0.004 0.033 1036 Dihedral : 8.280 89.868 1020 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.66 % Allowed : 21.22 % Favored : 75.11 % 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: 0.95 (0.31), residues: 739 helix: 2.16 (0.28), residues: 330 sheet: 0.20 (0.40), residues: 170 loop : -1.26 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.011 0.001 TYR A 451 PHE 0.022 0.001 PHE A 323 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6300) covalent geometry : angle 0.50615 ( 8548) SS BOND : bond 0.00552 ( 2) SS BOND : angle 1.01169 ( 4) hydrogen bonds : bond 0.04195 ( 327) hydrogen bonds : angle 4.11277 ( 921) link_BETA1-3 : bond 0.00474 ( 4) link_BETA1-3 : angle 2.22180 ( 12) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 1.52803 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.247 Fit side-chains REVERT: A 318 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 336 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.4501 (t80) REVERT: H 6 GLN cc_start: 0.8455 (mt0) cc_final: 0.7953 (tt0) REVERT: H 68 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8459 (ttpt) outliers start: 24 outliers final: 19 residues processed: 115 average time/residue: 0.0831 time to fit residues: 12.7795 Evaluate side-chains 114 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106657 restraints weight = 6867.582| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.55 r_work: 0.2808 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6310 Z= 0.153 Angle : 0.521 5.294 8576 Z= 0.267 Chirality : 0.040 0.135 955 Planarity : 0.004 0.032 1036 Dihedral : 8.035 87.661 1020 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.58 % Allowed : 21.22 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.31), residues: 739 helix: 2.19 (0.29), residues: 330 sheet: 0.29 (0.40), residues: 170 loop : -1.24 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.012 0.001 TYR H 98 PHE 0.022 0.001 PHE A 323 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6300) covalent geometry : angle 0.51188 ( 8548) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.07030 ( 4) hydrogen bonds : bond 0.04226 ( 327) hydrogen bonds : angle 4.08736 ( 921) link_BETA1-3 : bond 0.00437 ( 4) link_BETA1-3 : angle 2.10889 ( 12) link_BETA1-4 : bond 0.00638 ( 4) link_BETA1-4 : angle 1.58832 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.188 Fit side-chains REVERT: A 276 TYR cc_start: 0.8539 (m-80) cc_final: 0.8227 (m-80) REVERT: A 318 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8016 (p0) REVERT: A 336 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.4556 (t80) REVERT: H 6 GLN cc_start: 0.8427 (mt0) cc_final: 0.7911 (tt0) REVERT: H 68 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8475 (ttpt) outliers start: 30 outliers final: 27 residues processed: 118 average time/residue: 0.0775 time to fit residues: 12.4057 Evaluate side-chains 125 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.103041 restraints weight = 7111.194| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.69 r_work: 0.2802 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6310 Z= 0.128 Angle : 0.495 5.281 8576 Z= 0.254 Chirality : 0.039 0.132 955 Planarity : 0.004 0.031 1036 Dihedral : 7.770 84.243 1020 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.58 % Allowed : 21.37 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.31), residues: 739 helix: 2.27 (0.29), residues: 330 sheet: 0.46 (0.40), residues: 162 loop : -1.22 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.012 0.001 TYR A 451 PHE 0.021 0.001 PHE A 323 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6300) covalent geometry : angle 0.48556 ( 8548) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.75927 ( 4) hydrogen bonds : bond 0.03953 ( 327) hydrogen bonds : angle 4.00423 ( 921) link_BETA1-3 : bond 0.00441 ( 4) link_BETA1-3 : angle 2.08720 ( 12) link_BETA1-4 : bond 0.00564 ( 4) link_BETA1-4 : angle 1.52473 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.236 Fit side-chains REVERT: A 276 TYR cc_start: 0.8499 (m-80) cc_final: 0.8214 (m-80) REVERT: A 318 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.7963 (p0) REVERT: A 336 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.4674 (t80) REVERT: H 6 GLN cc_start: 0.8424 (mt0) cc_final: 0.7826 (tt0) REVERT: H 68 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8458 (ttpt) REVERT: H 78 SER cc_start: 0.8453 (m) cc_final: 0.8134 (t) outliers start: 30 outliers final: 25 residues processed: 118 average time/residue: 0.0772 time to fit residues: 12.2251 Evaluate side-chains 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.126359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.103387 restraints weight = 6988.452| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.59 r_work: 0.2798 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6310 Z= 0.152 Angle : 0.523 5.245 8576 Z= 0.267 Chirality : 0.040 0.136 955 Planarity : 0.004 0.034 1036 Dihedral : 7.611 79.517 1020 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.19 % Allowed : 20.92 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.31), residues: 739 helix: 2.23 (0.29), residues: 330 sheet: 0.34 (0.40), residues: 171 loop : -1.16 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.012 0.001 TYR A 451 PHE 0.022 0.001 PHE A 323 TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6300) covalent geometry : angle 0.51363 ( 8548) SS BOND : bond 0.00242 ( 2) SS BOND : angle 1.05570 ( 4) hydrogen bonds : bond 0.04199 ( 327) hydrogen bonds : angle 4.07345 ( 921) link_BETA1-3 : bond 0.00367 ( 4) link_BETA1-3 : angle 2.15683 ( 12) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 1.58428 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.244 Fit side-chains REVERT: A 276 TYR cc_start: 0.8554 (m-80) cc_final: 0.8295 (m-80) REVERT: A 318 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 336 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.4687 (t80) REVERT: A 504 MET cc_start: 0.7599 (tpt) cc_final: 0.7310 (tpt) REVERT: H 6 GLN cc_start: 0.8421 (mt0) cc_final: 0.7845 (tt0) REVERT: H 68 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8472 (ttpt) REVERT: H 78 SER cc_start: 0.8441 (m) cc_final: 0.8155 (t) REVERT: H 88 SER cc_start: 0.8988 (m) cc_final: 0.8498 (t) outliers start: 34 outliers final: 30 residues processed: 122 average time/residue: 0.0755 time to fit residues: 12.4255 Evaluate side-chains 127 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106185 restraints weight = 6955.513| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.56 r_work: 0.2823 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6310 Z= 0.120 Angle : 0.497 5.291 8576 Z= 0.254 Chirality : 0.039 0.141 955 Planarity : 0.003 0.032 1036 Dihedral : 7.285 74.582 1020 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.82 % Allowed : 22.44 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.31), residues: 739 helix: 2.33 (0.29), residues: 331 sheet: 0.48 (0.41), residues: 164 loop : -1.17 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.012 0.001 TYR A 451 PHE 0.022 0.001 PHE A 323 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6300) covalent geometry : angle 0.48823 ( 8548) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.87153 ( 4) hydrogen bonds : bond 0.03857 ( 327) hydrogen bonds : angle 3.98501 ( 921) link_BETA1-3 : bond 0.00446 ( 4) link_BETA1-3 : angle 2.03059 ( 12) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 1.53713 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.234 Fit side-chains REVERT: A 276 TYR cc_start: 0.8522 (m-80) cc_final: 0.8273 (m-80) REVERT: A 318 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.7986 (p0) REVERT: H 6 GLN cc_start: 0.8436 (mt0) cc_final: 0.7868 (tt0) REVERT: H 68 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8437 (ttpt) REVERT: H 78 SER cc_start: 0.8447 (m) cc_final: 0.8243 (p) REVERT: H 88 SER cc_start: 0.9012 (m) cc_final: 0.8532 (t) outliers start: 25 outliers final: 24 residues processed: 114 average time/residue: 0.0738 time to fit residues: 11.3193 Evaluate side-chains 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.126010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103268 restraints weight = 7004.127| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.57 r_work: 0.2797 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6310 Z= 0.164 Angle : 0.542 5.945 8576 Z= 0.276 Chirality : 0.041 0.143 955 Planarity : 0.004 0.032 1036 Dihedral : 7.235 69.059 1020 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.43 % Allowed : 21.83 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.31), residues: 739 helix: 2.19 (0.28), residues: 330 sheet: 0.46 (0.41), residues: 164 loop : -1.18 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 101 TYR 0.012 0.001 TYR H 98 PHE 0.021 0.001 PHE A 323 TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6300) covalent geometry : angle 0.53279 ( 8548) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.97406 ( 4) hydrogen bonds : bond 0.04309 ( 327) hydrogen bonds : angle 4.06020 ( 921) link_BETA1-3 : bond 0.00343 ( 4) link_BETA1-3 : angle 2.21507 ( 12) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 1.60885 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.212 Fit side-chains REVERT: A 276 TYR cc_start: 0.8525 (m-80) cc_final: 0.8279 (m-80) REVERT: A 318 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7971 (p0) REVERT: A 336 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.4488 (t80) REVERT: H 6 GLN cc_start: 0.8428 (mt0) cc_final: 0.7864 (tt0) REVERT: H 68 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8413 (ttpt) REVERT: H 88 SER cc_start: 0.9021 (m) cc_final: 0.8540 (t) outliers start: 29 outliers final: 26 residues processed: 113 average time/residue: 0.0735 time to fit residues: 11.0927 Evaluate side-chains 119 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.125080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.102010 restraints weight = 6987.435| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.60 r_work: 0.2808 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6310 Z= 0.142 Angle : 0.519 5.860 8576 Z= 0.265 Chirality : 0.040 0.145 955 Planarity : 0.004 0.033 1036 Dihedral : 6.920 63.297 1020 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.58 % Allowed : 21.98 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.31), residues: 739 helix: 2.24 (0.28), residues: 329 sheet: 0.52 (0.41), residues: 164 loop : -1.20 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.012 0.001 TYR A 451 PHE 0.021 0.001 PHE A 323 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6300) covalent geometry : angle 0.50993 ( 8548) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.81134 ( 4) hydrogen bonds : bond 0.04092 ( 327) hydrogen bonds : angle 4.02415 ( 921) link_BETA1-3 : bond 0.00396 ( 4) link_BETA1-3 : angle 2.12452 ( 12) link_BETA1-4 : bond 0.00576 ( 4) link_BETA1-4 : angle 1.57339 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.241 Fit side-chains REVERT: A 119 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7947 (mt-10) REVERT: A 276 TYR cc_start: 0.8514 (m-80) cc_final: 0.8278 (m-80) REVERT: A 318 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 336 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.4422 (t80) REVERT: H 6 GLN cc_start: 0.8416 (mt0) cc_final: 0.7839 (tt0) REVERT: H 68 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8398 (ttpt) outliers start: 30 outliers final: 27 residues processed: 111 average time/residue: 0.0795 time to fit residues: 11.9630 Evaluate side-chains 117 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.099758 restraints weight = 7052.049| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.57 r_work: 0.2820 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6310 Z= 0.137 Angle : 0.518 5.857 8576 Z= 0.264 Chirality : 0.040 0.138 955 Planarity : 0.004 0.033 1036 Dihedral : 6.625 56.160 1020 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.43 % Allowed : 22.29 % Favored : 73.28 % 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: 1.15 (0.31), residues: 739 helix: 2.25 (0.28), residues: 329 sheet: 0.49 (0.41), residues: 171 loop : -1.20 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.012 0.001 TYR A 451 PHE 0.022 0.001 PHE A 323 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6300) covalent geometry : angle 0.50857 ( 8548) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.85294 ( 4) hydrogen bonds : bond 0.04053 ( 327) hydrogen bonds : angle 4.00726 ( 921) link_BETA1-3 : bond 0.00389 ( 4) link_BETA1-3 : angle 2.12196 ( 12) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 1.56984 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.221 Fit side-chains REVERT: A 276 TYR cc_start: 0.8502 (m-80) cc_final: 0.8268 (m-80) REVERT: A 318 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 336 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.4428 (t80) REVERT: H 6 GLN cc_start: 0.8412 (mt0) cc_final: 0.7831 (tt0) REVERT: H 68 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8398 (ttpt) REVERT: H 88 SER cc_start: 0.9012 (m) cc_final: 0.8537 (t) outliers start: 29 outliers final: 27 residues processed: 111 average time/residue: 0.0778 time to fit residues: 11.7035 Evaluate side-chains 116 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.121272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.098343 restraints weight = 7040.617| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.58 r_work: 0.2798 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6310 Z= 0.157 Angle : 0.534 5.632 8576 Z= 0.272 Chirality : 0.040 0.137 955 Planarity : 0.004 0.033 1036 Dihedral : 6.484 55.812 1020 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.73 % Allowed : 22.14 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.31), residues: 739 helix: 2.19 (0.28), residues: 329 sheet: 0.45 (0.40), residues: 171 loop : -1.20 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.012 0.001 TYR H 98 PHE 0.022 0.001 PHE A 323 TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6300) covalent geometry : angle 0.52473 ( 8548) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.93633 ( 4) hydrogen bonds : bond 0.04270 ( 327) hydrogen bonds : angle 4.05740 ( 921) link_BETA1-3 : bond 0.00342 ( 4) link_BETA1-3 : angle 2.21117 ( 12) link_BETA1-4 : bond 0.00573 ( 4) link_BETA1-4 : angle 1.60027 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.90 seconds wall clock time: 29 minutes 43.19 seconds (1783.19 seconds total)