Starting phenix.real_space_refine on Thu Sep 10 21:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xrp_33416/09_2026/7xrp_33416.map" } resolution = 3.88 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= 0.011 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 14 5.16 5 C 2655 2.51 5 N 674 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 5 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1454 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 9, 'TRANS': 172} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.86, per 1000 atoms: 0.21 Number of scatterers: 4129 At special positions: 0 Unit cell: (73.91, 77.8, 113.588, 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 14 16.00 O 786 8.00 N 674 7.00 C 2655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.06 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 NAG-ASN " NAG A 401 " - " ASN A 165 " " NAG A 402 " - " ASN A 282 " " NAG A 403 " - " ASN A 122 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 104.2 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 5.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.510A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.959A pdb=" N PHE F 342 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 343 " --> pdb=" O GLY F 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 343' Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.708A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.761A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.590A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.713A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.562A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 69 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.601A pdb=" N THR B 122 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 124 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 121 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 92 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 39 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 99 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE B 33 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.601A pdb=" N THR B 122 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 124 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 121 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 92 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 357 removed outlier: 5.047A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU F 513 " --> pdb=" O CYS F 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 95 hydrogen bonds defined for protein. 219 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: 0.40 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 666 1.30 - 1.44: 1271 1.44 - 1.57: 2278 1.57 - 1.70: 1 1.70 - 1.83: 15 Bond restraints: 4231 Sorted by residual: bond pdb=" CA ALA F 352 " pdb=" C ALA F 352 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.04e-02 9.25e+03 6.82e+01 bond pdb=" CA SER F 349 " pdb=" C SER F 349 " ideal model delta sigma weight residual 1.526 1.425 0.100 1.36e-02 5.41e+03 5.46e+01 bond pdb=" CA ARG F 346 " pdb=" C ARG F 346 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.23e-02 6.61e+03 3.81e+01 bond pdb=" CA PHE F 347 " pdb=" C PHE F 347 " ideal model delta sigma weight residual 1.522 1.449 0.074 1.23e-02 6.61e+03 3.58e+01 bond pdb=" CA ALA F 348 " pdb=" C ALA F 348 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.38e-02 5.25e+03 2.71e+01 ... (remaining 4226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.09: 5709 5.09 - 10.19: 34 10.19 - 15.28: 4 15.28 - 20.37: 0 20.37 - 25.46: 1 Bond angle restraints: 5748 Sorted by residual: angle pdb=" N ARG A 214 " pdb=" CA ARG A 214 " pdb=" C ARG A 214 " ideal model delta sigma weight residual 109.76 84.30 25.46 1.59e+00 3.96e-01 2.56e+02 angle pdb=" N VAL F 350 " pdb=" CA VAL F 350 " pdb=" C VAL F 350 " ideal model delta sigma weight residual 110.62 118.46 -7.84 1.02e+00 9.61e-01 5.90e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" C ASN A 122 " ideal model delta sigma weight residual 111.28 118.92 -7.64 1.09e+00 8.42e-01 4.91e+01 angle pdb=" N TYR F 473 " pdb=" CA TYR F 473 " pdb=" C TYR F 473 " ideal model delta sigma weight residual 113.38 121.61 -8.23 1.23e+00 6.61e-01 4.47e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 113.10 107.19 5.91 9.70e-01 1.06e+00 3.72e+01 ... (remaining 5743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2135 17.34 - 34.67: 241 34.67 - 52.01: 45 52.01 - 69.35: 5 69.35 - 86.68: 4 Dihedral angle restraints: 2430 sinusoidal: 938 harmonic: 1492 Sorted by residual: dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -148.94 -31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASN F 360 " pdb=" C ASN F 360 " pdb=" N CYS F 361 " pdb=" CA CYS F 361 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE F 490 " pdb=" C PHE F 490 " pdb=" N PRO F 491 " pdb=" CA PRO F 491 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 546 0.095 - 0.190: 71 0.190 - 0.284: 14 0.284 - 0.379: 4 0.379 - 0.474: 4 Chirality restraints: 639 Sorted by residual: chirality pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" C PRO A 217 " pdb=" CB PRO A 217 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA PHE F 429 " pdb=" N PHE F 429 " pdb=" C PHE F 429 " pdb=" CB PHE F 429 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA VAL F 350 " pdb=" N VAL F 350 " pdb=" C VAL F 350 " pdb=" CB VAL F 350 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 636 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A 403 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " -0.135 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.316 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG A 401 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " -0.276 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG F 601 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " 0.385 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.000 2.00e-02 2.50e+03 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1059 2.79 - 3.32: 3382 3.32 - 3.84: 6407 3.84 - 4.37: 6913 4.37 - 4.90: 12570 Nonbonded interactions: 30331 Sorted by model distance: nonbonded pdb=" O THR A 51 " pdb=" OG1 THR A 274 " model vdw 2.261 3.040 nonbonded pdb=" N ARG A 214 " pdb=" O ARG A 214 " model vdw 2.271 2.496 nonbonded pdb=" O ASP A 290 " pdb=" OG SER A 297 " model vdw 2.277 3.040 nonbonded pdb=" OG SER F 383 " pdb=" O THR F 385 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 103 " pdb=" OG SER B 103 " model vdw 2.286 3.040 ... (remaining 30326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.060 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 4240 Z= 0.489 Angle : 1.144 25.464 5770 Z= 0.702 Chirality : 0.079 0.474 639 Planarity : 0.019 0.297 735 Dihedral : 14.630 86.684 1463 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.45 % Allowed : 12.87 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.63 (0.29), residues: 499 helix: -5.03 (0.29), residues: 24 sheet: -3.31 (0.33), residues: 154 loop : -2.90 (0.28), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 457 TYR 0.020 0.002 TYR F 351 PHE 0.036 0.002 PHE F 400 TRP 0.029 0.003 TRP F 436 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.49 ( 4231) covalent geometry : angle 1.13860 / 0.70 ( 5748) SS BOND : bond 0.01196 / 0.88 ( 5) SS BOND : angle 2.83083 / 1.60 ( 10) hydrogen bonds : bond 0.31823 / 21.27 ( 92) hydrogen bonds : angle 10.91849 / 7.16 ( 219) link_NAG-ASN : bond 0.00206 / 0.10 ( 4) link_NAG-ASN : angle 1.39048 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7900 (mttm) cc_final: 0.7665 (tmtt) REVERT: B 39 GLN cc_start: 0.6561 (tt0) cc_final: 0.6259 (pp30) REVERT: B 115 TRP cc_start: 0.7598 (m100) cc_final: 0.7102 (m100) REVERT: F 355 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8164 (ttt-90) REVERT: F 449 TYR cc_start: 0.8004 (m-80) cc_final: 0.7562 (m-80) REVERT: F 456 PHE cc_start: 0.8398 (m-80) cc_final: 0.8031 (m-80) REVERT: F 498 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7866 (mm-40) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1046 time to fit residues: 15.7443 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118888 restraints weight = 6453.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122073 restraints weight = 4906.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122963 restraints weight = 3338.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124715 restraints weight = 2787.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124788 restraints weight = 2416.251| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.004 0.032 4240 Z= 0.167 Angle : 0.707 7.937 5770 Z= 0.362 Chirality : 0.046 0.165 639 Planarity : 0.005 0.062 735 Dihedral : 5.632 27.890 562 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.84 % Allowed : 19.64 % Favored : 76.52 % 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 are not related in a simple way. whole: -4.04 (0.33), residues: 499 helix: -4.52 (0.44), residues: 30 sheet: -2.70 (0.33), residues: 186 loop : -2.45 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 466 TYR 0.015 0.001 TYR B 80 PHE 0.021 0.002 PHE A 168 TRP 0.018 0.002 TRP F 436 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 4231) covalent geometry : angle 0.69542 / 0.36 ( 5748) SS BOND : bond 0.00574 / 0.40 ( 5) SS BOND : angle 1.26960 / 0.74 ( 10) hydrogen bonds : bond 0.04399 / 2.97 ( 92) hydrogen bonds : angle 7.67781 / 5.14 ( 219) link_NAG-ASN : bond 0.00337 / 0.16 ( 4) link_NAG-ASN : angle 2.69664 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.130 Fit side-chains REVERT: A 41 LYS cc_start: 0.7946 (mttm) cc_final: 0.7672 (tmtt) REVERT: A 91 TYR cc_start: 0.9074 (t80) cc_final: 0.8828 (t80) REVERT: A 227 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 275 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: B 20 LEU cc_start: 0.8574 (mm) cc_final: 0.8273 (mm) REVERT: B 38 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7232 (tmm-80) REVERT: B 39 GLN cc_start: 0.6310 (tt0) cc_final: 0.5471 (pp30) REVERT: B 46 GLU cc_start: 0.6948 (tp30) cc_final: 0.6656 (tp30) REVERT: B 95 TYR cc_start: 0.8226 (m-80) cc_final: 0.7846 (m-80) REVERT: B 115 TRP cc_start: 0.7642 (m100) cc_final: 0.7335 (m100) REVERT: F 355 ARG cc_start: 0.8285 (ttt90) cc_final: 0.7870 (ttt-90) REVERT: F 364 ASP cc_start: 0.7944 (p0) cc_final: 0.7593 (p0) REVERT: F 417 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7934 (ttpp) REVERT: F 444 LYS cc_start: 0.7159 (tptp) cc_final: 0.6846 (tptp) REVERT: F 449 TYR cc_start: 0.7897 (m-80) cc_final: 0.7348 (m-80) REVERT: F 456 PHE cc_start: 0.8420 (m-80) cc_final: 0.8086 (m-80) REVERT: F 465 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: F 498 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7717 (mm-40) outliers start: 17 outliers final: 8 residues processed: 121 average time/residue: 0.0873 time to fit residues: 12.5118 Evaluate side-chains 98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124572 restraints weight = 6417.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126962 restraints weight = 3763.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128142 restraints weight = 3343.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129424 restraints weight = 2564.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130342 restraints weight = 2302.441| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4240 Z= 0.130 Angle : 0.625 7.055 5770 Z= 0.325 Chirality : 0.044 0.156 639 Planarity : 0.005 0.055 735 Dihedral : 5.151 24.545 562 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.51 % Allowed : 21.44 % Favored : 74.04 % 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 are not related in a simple way. whole: -3.77 (0.33), residues: 499 helix: -4.27 (0.49), residues: 30 sheet: -2.43 (0.34), residues: 186 loop : -2.34 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 466 TYR 0.021 0.001 TYR A 170 PHE 0.019 0.001 PHE F 338 TRP 0.012 0.001 TRP F 353 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4231) covalent geometry : angle 0.61853 / 0.32 ( 5748) SS BOND : bond 0.00358 / 0.16 ( 5) SS BOND : angle 1.48918 / 0.85 ( 10) hydrogen bonds : bond 0.03419 / 2.32 ( 92) hydrogen bonds : angle 6.93838 / 4.68 ( 219) link_NAG-ASN : bond 0.00192 / 0.08 ( 4) link_NAG-ASN : angle 1.71969 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.115 Fit side-chains REVERT: A 41 LYS cc_start: 0.8029 (mttm) cc_final: 0.7694 (tmtt) REVERT: A 129 LYS cc_start: 0.7290 (ttpt) cc_final: 0.6832 (tttm) REVERT: A 170 TYR cc_start: 0.7401 (t80) cc_final: 0.7180 (t80) REVERT: B 20 LEU cc_start: 0.8626 (mm) cc_final: 0.8356 (mm) REVERT: B 38 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7273 (tmm-80) REVERT: B 39 GLN cc_start: 0.6183 (tt0) cc_final: 0.5437 (pp30) REVERT: B 46 GLU cc_start: 0.6821 (tp30) cc_final: 0.6540 (tp30) REVERT: B 95 TYR cc_start: 0.8227 (m-80) cc_final: 0.7866 (m-80) REVERT: B 115 TRP cc_start: 0.7621 (m100) cc_final: 0.7357 (m100) REVERT: F 355 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7805 (ttm-80) REVERT: F 417 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7881 (ttpp) REVERT: F 421 TYR cc_start: 0.8287 (m-80) cc_final: 0.7923 (m-80) REVERT: F 444 LYS cc_start: 0.7186 (tptp) cc_final: 0.6858 (tptp) REVERT: F 449 TYR cc_start: 0.7836 (m-80) cc_final: 0.7267 (m-80) REVERT: F 498 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7719 (mm-40) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 0.0887 time to fit residues: 11.2102 Evaluate side-chains 99 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125969 restraints weight = 6318.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128410 restraints weight = 3767.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129370 restraints weight = 3364.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130423 restraints weight = 2543.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132367 restraints weight = 2233.788| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4240 Z= 0.119 Angle : 0.605 11.452 5770 Z= 0.306 Chirality : 0.044 0.153 639 Planarity : 0.004 0.042 735 Dihedral : 4.801 22.920 562 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.39 % Allowed : 25.28 % Favored : 71.33 % 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 are not related in a simple way. whole: -3.61 (0.34), residues: 499 helix: -4.13 (0.51), residues: 30 sheet: -2.37 (0.34), residues: 187 loop : -2.20 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 466 TYR 0.017 0.001 TYR F 369 PHE 0.019 0.001 PHE F 338 TRP 0.012 0.001 TRP F 353 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4231) covalent geometry : angle 0.60060 / 0.31 ( 5748) SS BOND : bond 0.00232 / 0.12 ( 5) SS BOND : angle 1.20608 / 0.70 ( 10) hydrogen bonds : bond 0.02998 / 2.04 ( 92) hydrogen bonds : angle 6.46488 / 4.37 ( 219) link_NAG-ASN : bond 0.00174 / 0.07 ( 4) link_NAG-ASN : angle 1.41665 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.178 Fit side-chains REVERT: A 41 LYS cc_start: 0.8006 (mttm) cc_final: 0.7741 (tmtt) REVERT: A 129 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6986 (tttm) REVERT: A 170 TYR cc_start: 0.7280 (t80) cc_final: 0.7065 (t80) REVERT: B 20 LEU cc_start: 0.8615 (mm) cc_final: 0.8380 (mm) REVERT: B 38 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7318 (tmm-80) REVERT: B 95 TYR cc_start: 0.8202 (m-80) cc_final: 0.7758 (m-80) REVERT: F 355 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7764 (ttm-80) REVERT: F 417 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7880 (ttpp) REVERT: F 444 LYS cc_start: 0.7174 (tptp) cc_final: 0.6880 (tptp) REVERT: F 449 TYR cc_start: 0.7781 (m-80) cc_final: 0.7280 (m-80) REVERT: F 498 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7746 (mm-40) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.0984 time to fit residues: 10.7853 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118629 restraints weight = 6507.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121444 restraints weight = 4068.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122736 restraints weight = 3373.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123493 restraints weight = 2589.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123844 restraints weight = 2445.594| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4240 Z= 0.265 Angle : 0.703 9.428 5770 Z= 0.363 Chirality : 0.047 0.149 639 Planarity : 0.005 0.059 735 Dihedral : 5.489 24.495 562 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.51 % Allowed : 25.96 % Favored : 69.53 % 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 are not related in a simple way. whole: -3.74 (0.34), residues: 499 helix: -4.29 (0.44), residues: 30 sheet: -2.58 (0.34), residues: 186 loop : -2.17 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 466 TYR 0.017 0.002 TYR F 453 PHE 0.023 0.002 PHE F 400 TRP 0.025 0.003 TRP F 436 HIS 0.001 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 ( 4231) covalent geometry : angle 0.69389 / 0.36 ( 5748) SS BOND : bond 0.00309 / 0.15 ( 5) SS BOND : angle 1.84836 / 1.04 ( 10) hydrogen bonds : bond 0.03752 / 2.56 ( 92) hydrogen bonds : angle 7.15111 / 4.86 ( 219) link_NAG-ASN : bond 0.00154 / 0.07 ( 4) link_NAG-ASN : angle 2.07244 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.135 Fit side-chains REVERT: A 91 TYR cc_start: 0.9161 (t80) cc_final: 0.8879 (t80) REVERT: A 170 TYR cc_start: 0.7213 (t80) cc_final: 0.6980 (t80) REVERT: A 229 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7124 (mm) REVERT: A 275 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: B 20 LEU cc_start: 0.8691 (mm) cc_final: 0.8352 (mm) REVERT: B 38 ARG cc_start: 0.8185 (ptm160) cc_final: 0.7381 (tmm-80) REVERT: B 46 GLU cc_start: 0.7179 (tp30) cc_final: 0.6959 (tp30) REVERT: F 364 ASP cc_start: 0.8089 (p0) cc_final: 0.7714 (p0) REVERT: F 417 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7914 (ttpp) REVERT: F 444 LYS cc_start: 0.7259 (tptp) cc_final: 0.6931 (tptp) REVERT: F 498 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7768 (mm-40) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.0899 time to fit residues: 10.6318 Evaluate side-chains 96 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121885 restraints weight = 6529.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124496 restraints weight = 3960.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125741 restraints weight = 3392.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126709 restraints weight = 2587.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127222 restraints weight = 2435.744| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4240 Z= 0.169 Angle : 0.627 8.042 5770 Z= 0.322 Chirality : 0.045 0.146 639 Planarity : 0.004 0.038 735 Dihedral : 5.066 23.350 562 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.06 % Allowed : 27.99 % Favored : 67.95 % 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 are not related in a simple way. whole: -3.62 (0.35), residues: 499 helix: -4.08 (0.50), residues: 30 sheet: -2.55 (0.34), residues: 186 loop : -2.07 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 466 TYR 0.020 0.002 TYR A 265 PHE 0.017 0.002 PHE F 400 TRP 0.015 0.002 TRP F 436 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 4231) covalent geometry : angle 0.62052 / 0.32 ( 5748) SS BOND : bond 0.00387 / 0.15 ( 5) SS BOND : angle 1.40062 / 0.80 ( 10) hydrogen bonds : bond 0.03123 / 2.13 ( 92) hydrogen bonds : angle 6.66603 / 4.54 ( 219) link_NAG-ASN : bond 0.00179 / 0.08 ( 4) link_NAG-ASN : angle 1.63591 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.172 Fit side-chains REVERT: A 229 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (mm) REVERT: A 275 PHE cc_start: 0.8350 (m-10) cc_final: 0.7736 (m-10) REVERT: B 20 LEU cc_start: 0.8682 (mm) cc_final: 0.8376 (mm) REVERT: B 38 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7428 (tmm-80) REVERT: F 417 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7938 (ttpp) REVERT: F 444 LYS cc_start: 0.7273 (tptp) cc_final: 0.6927 (tptp) REVERT: F 498 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7763 (mm-40) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.0922 time to fit residues: 10.0498 Evaluate side-chains 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122937 restraints weight = 6562.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126208 restraints weight = 4009.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127524 restraints weight = 3203.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128565 restraints weight = 2461.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128792 restraints weight = 2309.656| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4240 Z= 0.150 Angle : 0.608 7.196 5770 Z= 0.313 Chirality : 0.044 0.146 639 Planarity : 0.004 0.039 735 Dihedral : 4.875 22.948 562 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.74 % Allowed : 28.67 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.35), residues: 499 helix: -3.95 (0.52), residues: 30 sheet: -2.50 (0.34), residues: 186 loop : -2.00 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.016 0.001 TYR A 265 PHE 0.016 0.001 PHE F 400 TRP 0.013 0.001 TRP F 353 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 4231) covalent geometry : angle 0.60369 / 0.31 ( 5748) SS BOND : bond 0.00280 / 0.12 ( 5) SS BOND : angle 1.25190 / 0.73 ( 10) hydrogen bonds : bond 0.02957 / 1.99 ( 92) hydrogen bonds : angle 6.49611 / 4.42 ( 219) link_NAG-ASN : bond 0.00185 / 0.08 ( 4) link_NAG-ASN : angle 1.45374 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.134 Fit side-chains REVERT: A 129 LYS cc_start: 0.7345 (tttt) cc_final: 0.7106 (tmtt) REVERT: A 229 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7074 (mm) REVERT: A 275 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: B 20 LEU cc_start: 0.8704 (mm) cc_final: 0.8436 (mm) REVERT: B 38 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7364 (tmm-80) REVERT: F 417 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7872 (ttpp) REVERT: F 444 LYS cc_start: 0.7265 (tptp) cc_final: 0.6969 (tptp) REVERT: F 449 TYR cc_start: 0.7798 (m-80) cc_final: 0.7335 (m-80) REVERT: F 498 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7710 (mm-40) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 0.0915 time to fit residues: 10.6158 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS F 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123345 restraints weight = 6397.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126188 restraints weight = 3886.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127260 restraints weight = 3304.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128397 restraints weight = 2525.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128862 restraints weight = 2321.149| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4240 Z= 0.153 Angle : 0.619 7.025 5770 Z= 0.318 Chirality : 0.045 0.146 639 Planarity : 0.004 0.044 735 Dihedral : 4.852 22.991 562 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.29 % Allowed : 28.89 % Favored : 66.82 % 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 are not related in a simple way. whole: -3.46 (0.35), residues: 499 helix: -3.77 (0.57), residues: 30 sheet: -2.44 (0.34), residues: 187 loop : -1.98 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 34 TYR 0.014 0.002 TYR A 265 PHE 0.019 0.001 PHE F 400 TRP 0.015 0.001 TRP F 436 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 4231) covalent geometry : angle 0.61402 / 0.32 ( 5748) SS BOND : bond 0.00258 / 0.12 ( 5) SS BOND : angle 1.27165 / 0.75 ( 10) hydrogen bonds : bond 0.02932 / 1.97 ( 92) hydrogen bonds : angle 6.40986 / 4.37 ( 219) link_NAG-ASN : bond 0.00167 / 0.08 ( 4) link_NAG-ASN : angle 1.46010 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.146 Fit side-chains REVERT: A 91 TYR cc_start: 0.9160 (t80) cc_final: 0.8839 (t80) REVERT: A 229 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7019 (mm) REVERT: A 275 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7680 (m-10) REVERT: B 20 LEU cc_start: 0.8701 (mm) cc_final: 0.8439 (mm) REVERT: B 30 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7730 (m-70) REVERT: B 38 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7361 (tmm-80) REVERT: F 417 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7934 (ttpp) REVERT: F 444 LYS cc_start: 0.7252 (tptp) cc_final: 0.6942 (tptp) REVERT: F 449 TYR cc_start: 0.7810 (m-80) cc_final: 0.7350 (m-80) REVERT: F 498 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7721 (mm-40) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.0809 time to fit residues: 9.1280 Evaluate side-chains 91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124336 restraints weight = 6485.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127231 restraints weight = 3891.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129059 restraints weight = 3146.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129721 restraints weight = 2348.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131656 restraints weight = 2096.830| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4240 Z= 0.134 Angle : 0.611 7.423 5770 Z= 0.314 Chirality : 0.044 0.144 639 Planarity : 0.004 0.034 735 Dihedral : 4.777 23.541 562 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.61 % Allowed : 30.47 % Favored : 65.91 % 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 are not related in a simple way. whole: -3.37 (0.35), residues: 499 helix: -3.61 (0.63), residues: 30 sheet: -2.39 (0.34), residues: 187 loop : -1.93 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.014 0.001 TYR A 265 PHE 0.019 0.001 PHE F 400 TRP 0.011 0.001 TRP F 436 HIS 0.008 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 4231) covalent geometry : angle 0.60760 / 0.31 ( 5748) SS BOND : bond 0.00262 / 0.12 ( 5) SS BOND : angle 1.16761 / 0.70 ( 10) hydrogen bonds : bond 0.02812 / 1.88 ( 92) hydrogen bonds : angle 6.22997 / 4.24 ( 219) link_NAG-ASN : bond 0.00176 / 0.08 ( 4) link_NAG-ASN : angle 1.34982 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.128 Fit side-chains REVERT: A 229 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7026 (mm) REVERT: A 275 PHE cc_start: 0.8282 (m-10) cc_final: 0.7661 (m-10) REVERT: B 20 LEU cc_start: 0.8716 (mm) cc_final: 0.8474 (mm) REVERT: B 38 ARG cc_start: 0.8127 (ptm160) cc_final: 0.7403 (tmm-80) REVERT: F 417 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7918 (ttpp) REVERT: F 444 LYS cc_start: 0.7257 (tptp) cc_final: 0.6955 (tptp) REVERT: F 498 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7698 (mm-40) outliers start: 16 outliers final: 14 residues processed: 90 average time/residue: 0.0919 time to fit residues: 9.9401 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127408 restraints weight = 6392.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130127 restraints weight = 3833.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132151 restraints weight = 3141.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132668 restraints weight = 2375.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135089 restraints weight = 2160.032| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4240 Z= 0.111 Angle : 0.591 7.569 5770 Z= 0.304 Chirality : 0.045 0.178 639 Planarity : 0.004 0.032 735 Dihedral : 4.589 26.296 562 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.39 % Allowed : 29.57 % Favored : 67.04 % 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 are not related in a simple way. whole: -3.23 (0.35), residues: 499 helix: -3.66 (0.71), residues: 24 sheet: -2.39 (0.35), residues: 176 loop : -1.85 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 454 TYR 0.013 0.001 TYR A 265 PHE 0.014 0.001 PHE F 400 TRP 0.008 0.001 TRP F 436 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 4231) covalent geometry : angle 0.58877 / 0.30 ( 5748) SS BOND : bond 0.00238 / 0.11 ( 5) SS BOND : angle 1.00957 / 0.61 ( 10) hydrogen bonds : bond 0.02666 / 1.77 ( 92) hydrogen bonds : angle 5.83475 / 3.98 ( 219) link_NAG-ASN : bond 0.00231 / 0.11 ( 4) link_NAG-ASN : angle 1.04377 / 0.63 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.110 Fit side-chains REVERT: A 129 LYS cc_start: 0.6842 (tmtt) cc_final: 0.6456 (tptp) REVERT: A 275 PHE cc_start: 0.8208 (m-10) cc_final: 0.7655 (m-10) REVERT: B 20 LEU cc_start: 0.8647 (mm) cc_final: 0.8438 (mm) REVERT: B 38 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7485 (tmm-80) REVERT: F 417 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7819 (ttpp) REVERT: F 444 LYS cc_start: 0.7200 (tptp) cc_final: 0.6946 (tptp) REVERT: F 498 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7672 (mm-40) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.0809 time to fit residues: 8.9690 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.0030 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.0010 chunk 41 optimal weight: 0.0020 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129635 restraints weight = 6466.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131879 restraints weight = 3932.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132962 restraints weight = 3636.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133892 restraints weight = 2686.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135300 restraints weight = 2370.875| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4240 Z= 0.110 Angle : 0.609 7.566 5770 Z= 0.315 Chirality : 0.045 0.173 639 Planarity : 0.004 0.037 735 Dihedral : 4.438 23.518 562 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.71 % Allowed : 30.47 % Favored : 66.82 % 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 are not related in a simple way. whole: -3.16 (0.35), residues: 499 helix: -3.54 (0.74), residues: 24 sheet: -2.27 (0.35), residues: 174 loop : -1.86 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 454 TYR 0.014 0.001 TYR A 265 PHE 0.012 0.001 PHE F 400 TRP 0.007 0.001 TRP F 353 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 4231) covalent geometry : angle 0.60758 / 0.32 ( 5748) SS BOND : bond 0.00214 / 0.10 ( 5) SS BOND : angle 0.98119 / 0.61 ( 10) hydrogen bonds : bond 0.02650 / 1.77 ( 92) hydrogen bonds : angle 5.61169 / 3.83 ( 219) link_NAG-ASN : bond 0.00209 / 0.10 ( 4) link_NAG-ASN : angle 0.98446 / 0.59 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.25 seconds wall clock time: 18 minutes 30.78 seconds (1110.78 seconds total)