Starting phenix.real_space_refine on Tue Mar 3 12:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xrp_33416/03_2026/7xrp_33416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xrp_33416/03_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_33416/03_2026/7xrp_33416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xrp_33416/03_2026/7xrp_33416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xrp_33416/03_2026/7xrp_33416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xrp_33416/03_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-dev-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.03, per 1000 atoms: 0.25 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: 0.33 Conformation dependent library (CDL) restraints added in 144.8 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: 0.18 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: 0.68 Time building geometry restraints manager: 0.47 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: 2217 17.34 - 34.67: 241 34.67 - 52.01: 47 52.01 - 69.35: 5 69.35 - 86.68: 4 Dihedral angle restraints: 2514 sinusoidal: 1022 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 2511 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: 7.960 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.310 Find NCS groups from input model: 0.010 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 14.361 86.684 1547 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 covalent geometry : bond 0.00788 ( 4231) covalent geometry : angle 1.13860 ( 5748) SS BOND : bond 0.01196 ( 5) SS BOND : angle 2.83083 ( 10) hydrogen bonds : bond 0.31823 ( 92) hydrogen bonds : angle 10.91849 ( 219) link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 1.39048 ( 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 : 0.163 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: 0.1065 time to fit residues: 15.9573 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 : 0.149 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3796 r_free = 0.3796 target = 0.149530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119186 restraints weight = 6445.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121597 restraints weight = 4829.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122682 restraints weight = 3533.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123412 restraints weight = 2877.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123844 restraints weight = 2691.461| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4240 Z= 0.167 Angle : 0.703 8.847 5770 Z= 0.360 Chirality : 0.046 0.164 639 Planarity : 0.005 0.062 735 Dihedral : 6.695 58.866 646 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.29 % Allowed : 18.96 % Favored : 76.75 % 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: -4.02 (0.33), residues: 499 helix: -4.50 (0.44), residues: 30 sheet: -2.69 (0.33), residues: 186 loop : -2.43 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00387 ( 4231) covalent geometry : angle 0.69297 ( 5748) SS BOND : bond 0.00646 ( 5) SS BOND : angle 1.16063 ( 10) hydrogen bonds : bond 0.04088 ( 92) hydrogen bonds : angle 7.58027 ( 219) link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 2.58612 ( 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 129 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.146 Fit side-chains REVERT: A 41 LYS cc_start: 0.7949 (mttm) cc_final: 0.7669 (tmtt) REVERT: A 227 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8457 (m) REVERT: A 275 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: B 20 LEU cc_start: 0.8525 (mm) cc_final: 0.8212 (mm) REVERT: B 38 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7203 (tmm-80) REVERT: B 39 GLN cc_start: 0.6290 (tt0) cc_final: 0.5465 (pp30) REVERT: B 46 GLU cc_start: 0.6903 (tp30) cc_final: 0.6643 (tp30) REVERT: B 95 TYR cc_start: 0.8243 (m-80) cc_final: 0.7865 (m-80) REVERT: B 115 TRP cc_start: 0.7662 (m100) cc_final: 0.7374 (m100) REVERT: F 338 PHE cc_start: 0.8147 (p90) cc_final: 0.7884 (p90) REVERT: F 355 ARG cc_start: 0.8276 (ttt90) cc_final: 0.7900 (ttm-80) REVERT: F 364 ASP cc_start: 0.7994 (p0) cc_final: 0.7644 (p0) REVERT: F 417 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7945 (ttpp) REVERT: F 421 TYR cc_start: 0.8423 (m-10) cc_final: 0.8198 (m-80) REVERT: F 444 LYS cc_start: 0.7160 (tptp) cc_final: 0.6843 (tptp) REVERT: F 449 TYR cc_start: 0.7894 (m-80) cc_final: 0.7375 (m-80) REVERT: F 456 PHE cc_start: 0.8421 (m-80) cc_final: 0.8097 (m-80) REVERT: F 465 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: F 498 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7717 (mm-40) outliers start: 19 outliers final: 9 residues processed: 123 average time/residue: 0.1056 time to fit residues: 15.2694 Evaluate side-chains 101 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3835 r_free = 0.3835 target = 0.153523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124295 restraints weight = 6395.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127127 restraints weight = 3658.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129122 restraints weight = 2957.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129579 restraints weight = 2283.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130304 restraints weight = 2080.098| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2974 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= 0.137 Angle : 0.627 8.401 5770 Z= 0.324 Chirality : 0.044 0.156 639 Planarity : 0.005 0.052 735 Dihedral : 5.480 37.721 646 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.06 % Allowed : 22.57 % Favored : 73.36 % 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 (0.33), residues: 499 helix: -4.27 (0.49), residues: 30 sheet: -2.40 (0.34), residues: 186 loop : -2.33 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 466 TYR 0.023 0.002 TYR A 170 PHE 0.014 0.001 PHE F 338 TRP 0.014 0.001 TRP F 436 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4231) covalent geometry : angle 0.61923 ( 5748) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.50096 ( 10) hydrogen bonds : bond 0.03458 ( 92) hydrogen bonds : angle 6.84710 ( 219) link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 1.88792 ( 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 109 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.164 Fit side-chains REVERT: A 41 LYS cc_start: 0.8005 (mttm) cc_final: 0.7684 (tmtt) REVERT: A 91 TYR cc_start: 0.9028 (t80) cc_final: 0.8815 (t80) REVERT: A 129 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6967 (tttm) REVERT: A 170 TYR cc_start: 0.7385 (t80) cc_final: 0.7109 (t80) REVERT: B 20 LEU cc_start: 0.8639 (mm) cc_final: 0.8390 (mm) REVERT: B 38 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7320 (tmm-80) REVERT: B 39 GLN cc_start: 0.6185 (tt0) cc_final: 0.5535 (pp30) REVERT: B 46 GLU cc_start: 0.6849 (tp30) cc_final: 0.6606 (tp30) REVERT: B 95 TYR cc_start: 0.8212 (m-80) cc_final: 0.7821 (m-80) REVERT: B 115 TRP cc_start: 0.7644 (m100) cc_final: 0.7427 (m100) REVERT: F 408 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7143 (ptp90) REVERT: F 417 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7902 (ttpp) REVERT: F 444 LYS cc_start: 0.7216 (tptp) cc_final: 0.6889 (tptp) REVERT: F 449 TYR cc_start: 0.7825 (m-80) cc_final: 0.7311 (m-80) REVERT: F 498 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7718 (mm-40) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.0951 time to fit residues: 11.5093 Evaluate side-chains 96 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125155 restraints weight = 6378.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127353 restraints weight = 3773.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128698 restraints weight = 3384.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129854 restraints weight = 2572.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130718 restraints weight = 2338.450| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3418 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= 0.127 Angle : 0.609 11.586 5770 Z= 0.308 Chirality : 0.044 0.153 639 Planarity : 0.004 0.040 735 Dihedral : 5.401 45.676 646 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.06 % Allowed : 23.48 % Favored : 72.46 % 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: -3.57 (0.34), residues: 499 helix: -4.12 (0.50), residues: 30 sheet: -2.39 (0.33), residues: 192 loop : -2.12 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 466 TYR 0.017 0.001 TYR F 369 PHE 0.018 0.001 PHE F 338 TRP 0.012 0.001 TRP F 436 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4231) covalent geometry : angle 0.60204 ( 5748) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.30850 ( 10) hydrogen bonds : bond 0.02931 ( 92) hydrogen bonds : angle 6.53752 ( 219) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 1.83163 ( 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 104 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.166 Fit side-chains REVERT: A 41 LYS cc_start: 0.8002 (mttm) cc_final: 0.7715 (tmtt) REVERT: A 129 LYS cc_start: 0.7453 (ttpt) cc_final: 0.6976 (tttm) REVERT: A 170 TYR cc_start: 0.7167 (t80) cc_final: 0.6961 (t80) REVERT: B 20 LEU cc_start: 0.8629 (mm) cc_final: 0.8316 (mm) REVERT: B 38 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7280 (tmm-80) REVERT: B 95 TYR cc_start: 0.8160 (m-80) cc_final: 0.7692 (m-80) REVERT: F 417 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7951 (ttpp) REVERT: F 444 LYS cc_start: 0.7164 (tptp) cc_final: 0.6871 (tptp) REVERT: F 449 TYR cc_start: 0.7792 (m-80) cc_final: 0.7267 (m-80) REVERT: F 465 GLU cc_start: 0.8025 (tt0) cc_final: 0.7725 (tt0) REVERT: F 498 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7739 (mm-40) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.1067 time to fit residues: 12.3077 Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 31 LEU 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 402 ILE 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: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN F 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123648 restraints weight = 6400.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126383 restraints weight = 3758.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128467 restraints weight = 3055.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128795 restraints weight = 2336.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129644 restraints weight = 2149.960| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3565 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 9.477 5770 Z= 0.312 Chirality : 0.044 0.150 639 Planarity : 0.004 0.045 735 Dihedral : 5.610 50.089 646 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.97 % Allowed : 23.93 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.35), residues: 499 helix: -3.88 (0.57), residues: 30 sheet: -2.28 (0.35), residues: 186 loop : -2.07 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 466 TYR 0.014 0.001 TYR B 60 PHE 0.016 0.001 PHE F 338 TRP 0.015 0.001 TRP F 436 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4231) covalent geometry : angle 0.60115 ( 5748) SS BOND : bond 0.00265 ( 5) SS BOND : angle 1.35827 ( 10) hydrogen bonds : bond 0.02957 ( 92) hydrogen bonds : angle 6.48088 ( 219) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 1.83021 ( 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 108 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.166 Fit side-chains REVERT: A 41 LYS cc_start: 0.7997 (mttm) cc_final: 0.7763 (tmtt) REVERT: A 129 LYS cc_start: 0.7471 (ttpt) cc_final: 0.7014 (tttm) REVERT: A 275 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: B 20 LEU cc_start: 0.8679 (mm) cc_final: 0.8352 (mm) REVERT: B 38 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7398 (tmm-80) REVERT: F 417 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7967 (ttpp) REVERT: F 444 LYS cc_start: 0.7155 (tptp) cc_final: 0.6871 (tptp) REVERT: F 449 TYR cc_start: 0.7762 (m-80) cc_final: 0.7246 (m-80) REVERT: F 465 GLU cc_start: 0.8199 (tt0) cc_final: 0.7839 (tt0) REVERT: F 498 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7766 (mm-40) outliers start: 22 outliers final: 14 residues processed: 105 average time/residue: 0.1025 time to fit residues: 12.5899 Evaluate side-chains 92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 275 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 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS F 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124376 restraints weight = 6479.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126934 restraints weight = 3833.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128246 restraints weight = 3336.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129229 restraints weight = 2551.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129596 restraints weight = 2355.035| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3716 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= 0.138 Angle : 0.600 8.708 5770 Z= 0.309 Chirality : 0.044 0.145 639 Planarity : 0.004 0.034 735 Dihedral : 4.983 24.604 646 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.74 % Allowed : 24.60 % Favored : 70.65 % 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: -3.29 (0.35), residues: 499 helix: -3.73 (0.63), residues: 30 sheet: -2.21 (0.35), residues: 186 loop : -1.95 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 466 TYR 0.012 0.001 TYR B 60 PHE 0.018 0.001 PHE F 400 TRP 0.013 0.001 TRP F 436 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4231) covalent geometry : angle 0.59479 ( 5748) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.29366 ( 10) hydrogen bonds : bond 0.02839 ( 92) hydrogen bonds : angle 6.24316 ( 219) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.58388 ( 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 103 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.305 Fit side-chains REVERT: A 275 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: B 20 LEU cc_start: 0.8641 (mm) cc_final: 0.8350 (mm) REVERT: B 30 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7684 (m90) REVERT: B 38 ARG cc_start: 0.8071 (ptm160) cc_final: 0.7338 (tmm-80) REVERT: F 417 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7879 (ttpp) REVERT: F 444 LYS cc_start: 0.7229 (tptp) cc_final: 0.6957 (tptp) REVERT: F 449 TYR cc_start: 0.7764 (m-80) cc_final: 0.7299 (m-80) REVERT: F 465 GLU cc_start: 0.8116 (tt0) cc_final: 0.7887 (tt0) REVERT: F 498 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7778 (mm-40) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.0811 time to fit residues: 9.7878 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN 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 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 414 GLN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR 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: 0.9980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS F 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123999 restraints weight = 6555.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126769 restraints weight = 3977.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128146 restraints weight = 3340.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128990 restraints weight = 2563.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129756 restraints weight = 2403.361| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4240 Z= 0.155 Angle : 0.630 8.327 5770 Z= 0.322 Chirality : 0.044 0.147 639 Planarity : 0.004 0.036 735 Dihedral : 4.953 24.036 646 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.51 % Allowed : 25.06 % Favored : 70.43 % 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: -3.65 (0.65), residues: 30 sheet: -2.23 (0.36), residues: 180 loop : -1.89 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 454 TYR 0.028 0.001 TYR F 423 PHE 0.018 0.001 PHE F 400 TRP 0.014 0.001 TRP F 436 HIS 0.009 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4231) covalent geometry : angle 0.62406 ( 5748) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.25407 ( 10) hydrogen bonds : bond 0.02830 ( 92) hydrogen bonds : angle 6.24791 ( 219) link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 1.65352 ( 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 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.151 Fit side-chains REVERT: A 129 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7268 (tttt) REVERT: A 275 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: B 20 LEU cc_start: 0.8648 (mm) cc_final: 0.8376 (mm) REVERT: B 38 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7341 (tmm-80) REVERT: F 417 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7992 (ttpp) REVERT: F 449 TYR cc_start: 0.7777 (m-80) cc_final: 0.7285 (m-80) REVERT: F 465 GLU cc_start: 0.8100 (tt0) cc_final: 0.7886 (tt0) outliers start: 20 outliers final: 17 residues processed: 90 average time/residue: 0.0837 time to fit residues: 9.0969 Evaluate side-chains 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 31 LEU 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 495 TYR 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: 0.0980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS F 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126473 restraints weight = 6351.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129473 restraints weight = 3846.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130960 restraints weight = 3136.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131750 restraints weight = 2409.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132116 restraints weight = 2296.306| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4044 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= 0.124 Angle : 0.605 7.811 5770 Z= 0.311 Chirality : 0.044 0.145 639 Planarity : 0.004 0.031 735 Dihedral : 4.777 26.911 646 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.29 % Allowed : 24.60 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.35), residues: 499 helix: -3.64 (0.65), residues: 30 sheet: -2.08 (0.35), residues: 185 loop : -1.76 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 466 TYR 0.034 0.001 TYR A 170 PHE 0.019 0.001 PHE F 338 TRP 0.009 0.001 TRP F 436 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4231) covalent geometry : angle 0.60171 ( 5748) SS BOND : bond 0.00255 ( 5) SS BOND : angle 1.13318 ( 10) hydrogen bonds : bond 0.02652 ( 92) hydrogen bonds : angle 5.96549 ( 219) link_NAG-ASN : bond 0.00195 ( 4) link_NAG-ASN : angle 1.33090 ( 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 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.153 Fit side-chains REVERT: A 129 LYS cc_start: 0.7402 (ttpt) cc_final: 0.7119 (tmtt) REVERT: B 20 LEU cc_start: 0.8625 (mm) cc_final: 0.8391 (mm) REVERT: B 30 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7643 (m-70) REVERT: B 38 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7407 (tmm-80) REVERT: F 417 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7918 (ttpp) REVERT: F 449 TYR cc_start: 0.7754 (m-80) cc_final: 0.7251 (m-80) outliers start: 19 outliers final: 17 residues processed: 91 average time/residue: 0.0773 time to fit residues: 8.5068 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN 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 30 HIS Chi-restraints excluded: chain B residue 31 LEU 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 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: 0.5980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3854 r_free = 0.3854 target = 0.155318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126021 restraints weight = 6509.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129003 restraints weight = 3967.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130929 restraints weight = 3153.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131516 restraints weight = 2368.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132924 restraints weight = 2141.987| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4076 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= 0.138 Angle : 0.643 9.910 5770 Z= 0.330 Chirality : 0.045 0.199 639 Planarity : 0.004 0.033 735 Dihedral : 4.687 26.021 646 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.06 % Allowed : 24.83 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.36), residues: 499 helix: -3.21 (0.84), residues: 22 sheet: -2.05 (0.36), residues: 180 loop : -1.70 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 466 TYR 0.032 0.001 TYR F 423 PHE 0.019 0.001 PHE F 338 TRP 0.012 0.001 TRP F 436 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4231) covalent geometry : angle 0.63799 ( 5748) SS BOND : bond 0.00237 ( 5) SS BOND : angle 1.17908 ( 10) hydrogen bonds : bond 0.02676 ( 92) hydrogen bonds : angle 5.92664 ( 219) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 1.61472 ( 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 91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.244 Fit side-chains REVERT: A 129 LYS cc_start: 0.7459 (ttpt) cc_final: 0.7195 (tmtt) REVERT: B 20 LEU cc_start: 0.8607 (mm) cc_final: 0.8368 (mm) REVERT: F 417 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7874 (ttpp) REVERT: F 449 TYR cc_start: 0.7779 (m-80) cc_final: 0.7282 (m-80) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.0858 time to fit residues: 8.9610 Evaluate side-chains 86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN 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 31 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE 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: 0.7980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 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 = 0.3860 r_free = 0.3860 target = 0.155825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126461 restraints weight = 6404.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129313 restraints weight = 3901.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131135 restraints weight = 3225.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132016 restraints weight = 2425.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132323 restraints weight = 2283.964| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4187 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= 0.142 Angle : 0.678 13.101 5770 Z= 0.348 Chirality : 0.045 0.171 639 Planarity : 0.004 0.033 735 Dihedral : 4.727 24.906 646 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.39 % Allowed : 26.41 % Favored : 70.20 % Cbeta Deviations : 0.21 % 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: -2.89 (0.36), residues: 499 helix: -3.14 (0.84), residues: 22 sheet: -2.02 (0.36), residues: 180 loop : -1.74 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 357 TYR 0.034 0.002 TYR F 423 PHE 0.018 0.001 PHE F 338 TRP 0.012 0.001 TRP F 436 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4231) covalent geometry : angle 0.67271 ( 5748) SS BOND : bond 0.00242 ( 5) SS BOND : angle 1.17202 ( 10) hydrogen bonds : bond 0.02721 ( 92) hydrogen bonds : angle 5.91290 ( 219) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 1.69164 ( 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 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.137 Fit side-chains REVERT: A 129 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7193 (tmtt) REVERT: B 20 LEU cc_start: 0.8589 (mm) cc_final: 0.8347 (mm) REVERT: F 417 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7960 (ttpp) REVERT: F 449 TYR cc_start: 0.7799 (m-80) cc_final: 0.7288 (m-80) outliers start: 15 outliers final: 15 residues processed: 86 average time/residue: 0.0750 time to fit residues: 7.9411 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN 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 31 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE 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: 3.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.0020 chunk 41 optimal weight: 0.8980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129149 restraints weight = 6425.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131934 restraints weight = 3814.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133428 restraints weight = 3232.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134609 restraints weight = 2450.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135583 restraints weight = 2234.561| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4387 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= 0.117 Angle : 0.655 12.624 5770 Z= 0.335 Chirality : 0.045 0.171 639 Planarity : 0.004 0.034 735 Dihedral : 4.451 24.261 646 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.16 % Allowed : 26.19 % Favored : 70.65 % 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: -2.84 (0.35), residues: 499 helix: -3.00 (0.88), residues: 22 sheet: -1.97 (0.36), residues: 181 loop : -1.72 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 357 TYR 0.027 0.001 TYR A 170 PHE 0.019 0.001 PHE F 338 TRP 0.006 0.001 TRP F 353 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4231) covalent geometry : angle 0.65057 ( 5748) SS BOND : bond 0.00216 ( 5) SS BOND : angle 1.05522 ( 10) hydrogen bonds : bond 0.02578 ( 92) hydrogen bonds : angle 5.64719 ( 219) link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 1.61996 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1091.67 seconds wall clock time: 19 minutes 24.93 seconds (1164.93 seconds total)