Starting phenix.real_space_refine on Thu Jul 24 12:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smn_40594/07_2025/8smn_40594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smn_40594/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8smn_40594/07_2025/8smn_40594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smn_40594/07_2025/8smn_40594.map" model { file = "/net/cci-nas-00/data/ceres_data/8smn_40594/07_2025/8smn_40594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smn_40594/07_2025/8smn_40594.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.40, per 1000 atoms: 0.72 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: 1.75 Conformation dependent library (CDL) restraints added in 913.5 milliseconds 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: 0.74 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: 1.90 Time building geometry restraints manager: 2.05 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: 3.060 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.610 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.020 0.001 PHE A 323 TYR 0.010 0.001 TYR A 451 ARG 0.002 0.000 ARG H 90 Details of bonding type rmsd link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 1.69421 ( 12) hydrogen bonds : bond 0.13261 ( 327) hydrogen bonds : angle 5.42812 ( 921) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.51860 ( 4) link_BETA1-3 : bond 0.00264 ( 4) link_BETA1-3 : angle 1.73265 ( 12) covalent geometry : bond 0.00530 ( 6300) covalent geometry : angle 0.60591 ( 8548) *********************** 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 : 0.611 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: 0.2069 time to fit residues: 26.5718 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 : 0.696 ------------------------------------------------------------------------------- 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 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.4494 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105658 restraints weight = 6930.446| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.65 r_work: 0.2948 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6310 Z= 0.118 Angle : 0.503 5.285 8576 Z= 0.258 Chirality : 0.039 0.129 955 Planarity : 0.004 0.035 1036 Dihedral : 8.104 86.306 1022 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.75 % Allowed : 23.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.32), residues: 739 helix: 2.31 (0.29), residues: 330 sheet: 0.27 (0.41), residues: 183 loop : -1.26 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 401 PHE 0.021 0.001 PHE A 323 TYR 0.013 0.001 TYR A 451 ARG 0.002 0.000 ARG A 271 Details of bonding type rmsd link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 1.65870 ( 12) hydrogen bonds : bond 0.03789 ( 327) hydrogen bonds : angle 4.16464 ( 921) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.13880 ( 4) link_BETA1-3 : bond 0.00732 ( 4) link_BETA1-3 : angle 1.68980 ( 12) covalent geometry : bond 0.00260 ( 6300) covalent geometry : angle 0.49549 ( 8548) *********************** 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 : 0.652 Fit side-chains REVERT: A 318 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7721 (p0) REVERT: A 336 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.4729 (t80) REVERT: A 461 MET cc_start: 0.8842 (mmm) cc_final: 0.8503 (mmm) REVERT: H 10 SER cc_start: 0.8278 (t) cc_final: 0.7791 (m) REVERT: H 68 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8359 (ttpt) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.2060 time to fit residues: 31.2223 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 : 0.630 ------------------------------------------------------------------------------- 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 44 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.120105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.097020 restraints weight = 7111.411| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.57 r_work: 0.2772 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6310 Z= 0.227 Angle : 0.622 6.138 8576 Z= 0.317 Chirality : 0.044 0.143 955 Planarity : 0.005 0.038 1036 Dihedral : 8.592 86.718 1020 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.12 % Allowed : 21.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 739 helix: 1.89 (0.28), residues: 329 sheet: 0.27 (0.41), residues: 162 loop : -1.32 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 50 HIS 0.005 0.001 HIS A 401 PHE 0.023 0.002 PHE A 323 TYR 0.013 0.002 TYR H 98 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.73930 ( 12) hydrogen bonds : bond 0.05273 ( 327) hydrogen bonds : angle 4.37054 ( 921) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.24305 ( 4) link_BETA1-3 : bond 0.00360 ( 4) link_BETA1-3 : angle 2.56640 ( 12) covalent geometry : bond 0.00548 ( 6300) covalent geometry : angle 0.61107 ( 8548) *********************** 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 126 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.614 Fit side-chains REVERT: A 42 ILE cc_start: 0.8562 (mm) cc_final: 0.8341 (mt) REVERT: A 318 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.7953 (p0) REVERT: A 336 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.4526 (t80) REVERT: H 6 GLN cc_start: 0.8455 (mt0) cc_final: 0.7885 (tt0) REVERT: H 68 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8482 (ttpt) outliers start: 27 outliers final: 21 residues processed: 118 average time/residue: 0.1748 time to fit residues: 27.3824 Evaluate side-chains 119 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 556 VAL Chi-restraints excluded: chain A residue 564 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 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 = 0.3259 r_free = 0.3259 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098879 restraints weight = 7136.374| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.71 r_work: 0.2797 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1858 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= 0.129 Angle : 0.507 5.263 8576 Z= 0.261 Chirality : 0.039 0.134 955 Planarity : 0.004 0.033 1036 Dihedral : 7.926 84.885 1020 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.36 % Allowed : 22.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 739 helix: 2.12 (0.28), residues: 329 sheet: 0.41 (0.41), residues: 162 loop : -1.34 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS A 401 PHE 0.022 0.001 PHE A 323 TYR 0.013 0.001 TYR A 451 ARG 0.001 0.000 ARG H 90 Details of bonding type rmsd link_BETA1-4 : bond 0.00604 ( 4) link_BETA1-4 : angle 1.57636 ( 12) hydrogen bonds : bond 0.04089 ( 327) hydrogen bonds : angle 4.11637 ( 921) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.89353 ( 4) link_BETA1-3 : bond 0.00497 ( 4) link_BETA1-3 : angle 2.07680 ( 12) covalent geometry : bond 0.00294 ( 6300) covalent geometry : angle 0.49763 ( 8548) *********************** 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 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.689 Fit side-chains REVERT: A 42 ILE cc_start: 0.8583 (mm) cc_final: 0.8307 (mt) REVERT: A 240 ASP cc_start: 0.8283 (m-30) cc_final: 0.7999 (m-30) REVERT: A 276 TYR cc_start: 0.8535 (m-80) cc_final: 0.8234 (m-80) REVERT: A 318 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.7945 (p0) REVERT: A 336 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.4676 (t80) REVERT: H 6 GLN cc_start: 0.8444 (mt0) cc_final: 0.7909 (tt0) REVERT: H 68 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8473 (ttpt) outliers start: 22 outliers final: 18 residues processed: 113 average time/residue: 0.1902 time to fit residues: 28.3454 Evaluate side-chains 115 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 487 ASN 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 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.125182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.101199 restraints weight = 7079.579| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.70 r_work: 0.2905 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6310 Z= 0.104 Angle : 0.470 5.285 8576 Z= 0.242 Chirality : 0.038 0.131 955 Planarity : 0.003 0.031 1036 Dihedral : 7.459 80.103 1020 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.51 % Allowed : 22.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.31), residues: 739 helix: 2.36 (0.29), residues: 330 sheet: 0.45 (0.40), residues: 175 loop : -1.28 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS A 401 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR A 451 ARG 0.001 0.000 ARG H 90 Details of bonding type rmsd link_BETA1-4 : bond 0.00606 ( 4) link_BETA1-4 : angle 1.50653 ( 12) hydrogen bonds : bond 0.03620 ( 327) hydrogen bonds : angle 3.94707 ( 921) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.69322 ( 4) link_BETA1-3 : bond 0.00544 ( 4) link_BETA1-3 : angle 1.96547 ( 12) covalent geometry : bond 0.00225 ( 6300) covalent geometry : angle 0.46159 ( 8548) *********************** 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 116 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.709 Fit side-chains REVERT: A 276 TYR cc_start: 0.8543 (m-80) cc_final: 0.8282 (m-80) REVERT: A 318 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.7941 (p0) REVERT: A 336 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.4642 (t80) REVERT: H 6 GLN cc_start: 0.8457 (mt0) cc_final: 0.7896 (tt0) REVERT: H 68 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8452 (ttpt) REVERT: H 78 SER cc_start: 0.8378 (m) cc_final: 0.8039 (t) outliers start: 23 outliers final: 18 residues processed: 109 average time/residue: 0.1869 time to fit residues: 27.0654 Evaluate side-chains 111 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 453 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 92 GLU 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 18 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.127525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.104691 restraints weight = 6924.347| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.59 r_work: 0.2905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6310 Z= 0.117 Angle : 0.485 5.290 8576 Z= 0.248 Chirality : 0.039 0.130 955 Planarity : 0.004 0.034 1036 Dihedral : 7.236 74.746 1020 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.43 % Allowed : 21.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 739 helix: 2.41 (0.29), residues: 330 sheet: 0.42 (0.40), residues: 171 loop : -1.23 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.021 0.001 PHE A 323 TYR 0.011 0.001 TYR A 451 ARG 0.001 0.000 ARG H 90 Details of bonding type rmsd link_BETA1-4 : bond 0.00567 ( 4) link_BETA1-4 : angle 1.52919 ( 12) hydrogen bonds : bond 0.03737 ( 327) hydrogen bonds : angle 3.92336 ( 921) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.71301 ( 4) link_BETA1-3 : bond 0.00447 ( 4) link_BETA1-3 : angle 1.99855 ( 12) covalent geometry : bond 0.00268 ( 6300) covalent geometry : angle 0.47611 ( 8548) *********************** 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 124 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.840 Fit side-chains REVERT: A 276 TYR cc_start: 0.8526 (m-80) cc_final: 0.8274 (m-80) REVERT: A 318 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.7973 (p0) REVERT: A 336 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.4530 (t80) REVERT: H 6 GLN cc_start: 0.8462 (mt0) cc_final: 0.7912 (tt0) REVERT: H 68 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8412 (ttpt) REVERT: H 78 SER cc_start: 0.8443 (m) cc_final: 0.8151 (t) REVERT: H 88 SER cc_start: 0.8998 (m) cc_final: 0.8516 (t) outliers start: 29 outliers final: 24 residues processed: 115 average time/residue: 0.1981 time to fit residues: 31.4301 Evaluate side-chains 120 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 405 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.125631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.101533 restraints weight = 7024.669| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.69 r_work: 0.2904 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6310 Z= 0.105 Angle : 0.476 5.296 8576 Z= 0.243 Chirality : 0.038 0.128 955 Planarity : 0.003 0.036 1036 Dihedral : 6.935 69.455 1020 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.82 % Allowed : 21.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 739 helix: 2.48 (0.29), residues: 330 sheet: 0.52 (0.40), residues: 175 loop : -1.20 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 401 PHE 0.021 0.001 PHE A 323 TYR 0.011 0.001 TYR A 451 ARG 0.001 0.000 ARG A 28 Details of bonding type rmsd link_BETA1-4 : bond 0.00582 ( 4) link_BETA1-4 : angle 1.51289 ( 12) hydrogen bonds : bond 0.03572 ( 327) hydrogen bonds : angle 3.89754 ( 921) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.02315 ( 4) link_BETA1-3 : bond 0.00464 ( 4) link_BETA1-3 : angle 1.93551 ( 12) covalent geometry : bond 0.00233 ( 6300) covalent geometry : angle 0.46705 ( 8548) *********************** 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 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.745 Fit side-chains REVERT: A 71 LEU cc_start: 0.8450 (tp) cc_final: 0.8112 (mm) REVERT: A 276 TYR cc_start: 0.8523 (m-80) cc_final: 0.8279 (m-80) REVERT: A 318 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 504 MET cc_start: 0.7612 (tpt) cc_final: 0.7382 (tpt) REVERT: H 6 GLN cc_start: 0.8464 (mt0) cc_final: 0.7918 (tt0) REVERT: H 68 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8442 (ttpt) REVERT: H 78 SER cc_start: 0.8482 (m) cc_final: 0.8209 (t) REVERT: H 88 SER cc_start: 0.9003 (m) cc_final: 0.8514 (t) outliers start: 25 outliers final: 23 residues processed: 110 average time/residue: 0.1924 time to fit residues: 28.9548 Evaluate side-chains 115 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 351 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 405 THR 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 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 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.101787 restraints weight = 6960.197| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.58 r_work: 0.2838 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2186 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= 0.114 Angle : 0.484 5.276 8576 Z= 0.247 Chirality : 0.039 0.130 955 Planarity : 0.004 0.037 1036 Dihedral : 6.666 61.883 1020 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.12 % Allowed : 21.53 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 739 helix: 2.48 (0.29), residues: 330 sheet: 0.62 (0.41), residues: 168 loop : -1.22 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.022 0.001 PHE A 323 TYR 0.011 0.001 TYR A 451 ARG 0.001 0.000 ARG H 101 Details of bonding type rmsd link_BETA1-4 : bond 0.00563 ( 4) link_BETA1-4 : angle 1.51837 ( 12) hydrogen bonds : bond 0.03673 ( 327) hydrogen bonds : angle 3.89408 ( 921) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.91787 ( 4) link_BETA1-3 : bond 0.00406 ( 4) link_BETA1-3 : angle 1.97777 ( 12) covalent geometry : bond 0.00260 ( 6300) covalent geometry : angle 0.47567 ( 8548) *********************** 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 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.618 Fit side-chains REVERT: A 112 GLU cc_start: 0.7703 (tp30) cc_final: 0.7471 (tp30) REVERT: A 276 TYR cc_start: 0.8529 (m-80) cc_final: 0.8289 (m-80) REVERT: A 318 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8014 (p0) REVERT: A 336 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.4494 (t80) REVERT: A 504 MET cc_start: 0.7572 (tpt) cc_final: 0.7300 (tpt) REVERT: H 6 GLN cc_start: 0.8464 (mt0) cc_final: 0.7898 (tt0) REVERT: H 68 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8437 (ttpt) REVERT: H 78 SER cc_start: 0.8539 (m) cc_final: 0.8299 (p) REVERT: H 88 SER cc_start: 0.8986 (m) cc_final: 0.8493 (t) outliers start: 27 outliers final: 25 residues processed: 114 average time/residue: 0.3072 time to fit residues: 46.7567 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 : 0.804 ------------------------------------------------------------------------------- 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 108 GLN 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 405 THR 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 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 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.122700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.099483 restraints weight = 7028.211| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.59 r_work: 0.2807 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2294 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= 0.149 Angle : 0.524 5.225 8576 Z= 0.266 Chirality : 0.040 0.132 955 Planarity : 0.004 0.036 1036 Dihedral : 6.591 55.710 1020 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.12 % Allowed : 21.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 739 helix: 2.34 (0.29), residues: 330 sheet: 0.61 (0.40), residues: 168 loop : -1.24 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR H 98 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 1.57065 ( 12) hydrogen bonds : bond 0.04139 ( 327) hydrogen bonds : angle 3.99979 ( 921) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.03780 ( 4) link_BETA1-3 : bond 0.00330 ( 4) link_BETA1-3 : angle 2.11693 ( 12) covalent geometry : bond 0.00352 ( 6300) covalent geometry : angle 0.51474 ( 8548) *********************** 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 117 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.774 Fit side-chains REVERT: A 112 GLU cc_start: 0.7713 (tp30) cc_final: 0.7470 (tp30) REVERT: A 276 TYR cc_start: 0.8513 (m-80) cc_final: 0.8271 (m-80) REVERT: A 318 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8016 (p0) REVERT: A 336 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.4531 (t80) REVERT: A 504 MET cc_start: 0.7583 (tpt) cc_final: 0.7369 (tpt) REVERT: A 542 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.5928 (t80) REVERT: H 6 GLN cc_start: 0.8425 (mt0) cc_final: 0.7854 (tt0) REVERT: H 68 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8447 (ttpt) REVERT: H 78 SER cc_start: 0.8459 (m) cc_final: 0.8257 (p) REVERT: H 88 SER cc_start: 0.9002 (m) cc_final: 0.8529 (t) outliers start: 27 outliers final: 23 residues processed: 109 average time/residue: 0.2661 time to fit residues: 39.2131 Evaluate side-chains 115 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 405 THR 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 542 TYR 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 94 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 45 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 64 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.100057 restraints weight = 7059.011| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.70 r_work: 0.2809 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2317 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= 0.120 Angle : 0.499 5.835 8576 Z= 0.254 Chirality : 0.039 0.133 955 Planarity : 0.003 0.029 1036 Dihedral : 6.149 54.581 1020 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.12 % Allowed : 21.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.31), residues: 739 helix: 2.39 (0.29), residues: 330 sheet: 0.63 (0.40), residues: 168 loop : -1.20 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.021 0.001 PHE A 323 TYR 0.011 0.001 TYR A 451 ARG 0.001 0.000 ARG A 204 Details of bonding type rmsd link_BETA1-4 : bond 0.00621 ( 4) link_BETA1-4 : angle 1.55885 ( 12) hydrogen bonds : bond 0.03814 ( 327) hydrogen bonds : angle 3.94418 ( 921) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.92582 ( 4) link_BETA1-3 : bond 0.00394 ( 4) link_BETA1-3 : angle 2.01313 ( 12) covalent geometry : bond 0.00274 ( 6300) covalent geometry : angle 0.48997 ( 8548) ********************** 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 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.678 Fit side-chains REVERT: A 112 GLU cc_start: 0.7723 (tp30) cc_final: 0.7493 (tp30) REVERT: A 276 TYR cc_start: 0.8501 (m-80) cc_final: 0.8260 (m-80) REVERT: A 318 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8021 (p0) REVERT: A 336 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.4435 (t80) REVERT: A 504 MET cc_start: 0.7514 (tpt) cc_final: 0.7312 (tpt) REVERT: A 542 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.5899 (t80) REVERT: H 6 GLN cc_start: 0.8426 (mt0) cc_final: 0.7826 (tt0) REVERT: H 68 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8437 (ttpt) REVERT: H 78 SER cc_start: 0.8474 (m) cc_final: 0.8262 (p) REVERT: H 88 SER cc_start: 0.8993 (m) cc_final: 0.8513 (t) outliers start: 27 outliers final: 24 residues processed: 115 average time/residue: 0.1826 time to fit residues: 28.2306 Evaluate side-chains 121 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 405 THR 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 542 TYR 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 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 27 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.122941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.098668 restraints weight = 7153.689| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.70 r_work: 0.2793 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6310 Z= 0.143 Angle : 0.520 5.399 8576 Z= 0.265 Chirality : 0.040 0.135 955 Planarity : 0.004 0.029 1036 Dihedral : 5.984 55.264 1020 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.12 % Allowed : 22.29 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.31), residues: 739 helix: 2.32 (0.29), residues: 330 sheet: 0.64 (0.41), residues: 168 loop : -1.23 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.021 0.001 PHE A 323 TYR 0.013 0.001 TYR H 98 ARG 0.001 0.000 ARG A 204 Details of bonding type rmsd link_BETA1-4 : bond 0.00568 ( 4) link_BETA1-4 : angle 1.58468 ( 12) hydrogen bonds : bond 0.04093 ( 327) hydrogen bonds : angle 3.99440 ( 921) SS BOND : bond 0.00217 ( 2) SS BOND : angle 1.00468 ( 4) link_BETA1-3 : bond 0.00332 ( 4) link_BETA1-3 : angle 2.10798 ( 12) covalent geometry : bond 0.00338 ( 6300) covalent geometry : angle 0.51076 ( 8548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.32 seconds wall clock time: 65 minutes 27.11 seconds (3927.11 seconds total)