Starting phenix.real_space_refine on Tue Aug 4 15:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yt6_73443/08_2026/9yt6_73443.map" } resolution = 2.79 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= 0.013 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 18 5.16 5 C 2704 2.51 5 N 673 2.21 5 O 797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1957 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 4 Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2109 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 17, 'TRANS': 247} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: 1.24, per 1000 atoms: 0.30 Number of scatterers: 4192 At special positions: 0 Unit cell: (90.688, 76.544, 90.688, 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 18 16.00 O 797 8.00 N 673 7.00 C 2704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 230 " " NAG A1302 " - " ASN A 120 " " NAG A1303 " - " ASN A 241 " " NAG A1304 " - " ASN A 162 " " NAG B1301 " - " ASN B 331 " " NAG C 1 " - " ASN A 278 " " NAG D 1 " - " ASN B 354 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 164.4 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.5% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 153 through 156 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.670A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.846A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 7.860A pdb=" N ASN A 61 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 265 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 187 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N PHE A 198 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP A 224 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 200 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.275A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.885A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.969A pdb=" N GLY A 101 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 239 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 99 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 118 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 169 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 165 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.573A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 306 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: 0.60 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1279 1.34 - 1.46: 896 1.46 - 1.57: 2107 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 4303 Sorted by residual: bond pdb=" N PHE B 497 " pdb=" CA PHE B 497 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.41e-02 5.03e+03 5.08e+00 bond pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CA SER A 69 " pdb=" CB SER A 69 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.86e-02 2.89e+03 1.44e+00 bond pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.06e+00 bond pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 1.520 1.532 -0.013 1.23e-02 6.61e+03 1.03e+00 ... (remaining 4298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 5667 1.38 - 2.76: 127 2.76 - 4.14: 47 4.14 - 5.53: 4 5.53 - 6.91: 2 Bond angle restraints: 5847 Sorted by residual: angle pdb=" C PHE B 497 " pdb=" CA PHE B 497 " pdb=" CB PHE B 497 " ideal model delta sigma weight residual 112.11 116.24 -4.13 1.46e+00 4.69e-01 8.01e+00 angle pdb=" N ASP A 40 " pdb=" CA ASP A 40 " pdb=" C ASP A 40 " ideal model delta sigma weight residual 108.34 111.60 -3.26 1.31e+00 5.83e-01 6.18e+00 angle pdb=" CA PHE B 497 " pdb=" C PHE B 497 " pdb=" O PHE B 497 " ideal model delta sigma weight residual 122.03 118.98 3.05 1.25e+00 6.40e-01 5.97e+00 angle pdb=" CA GLU A 151 " pdb=" CB GLU A 151 " pdb=" CG GLU A 151 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.63e+00 angle pdb=" C SER A 69 " pdb=" CA SER A 69 " pdb=" CB SER A 69 " ideal model delta sigma weight residual 116.54 113.85 2.69 1.15e+00 7.56e-01 5.47e+00 ... (remaining 5842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 2350 16.61 - 33.22: 215 33.22 - 49.83: 54 49.83 - 66.44: 22 66.44 - 83.05: 5 Dihedral angle restraints: 2646 sinusoidal: 1161 harmonic: 1485 Sorted by residual: dihedral pdb=" CA GLU A 94 " pdb=" C GLU A 94 " pdb=" N LYS A 95 " pdb=" CA LYS A 95 " ideal model delta harmonic sigma weight residual 180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.51 -29.51 1 1.00e+01 1.00e-02 1.25e+01 dihedral pdb=" C PHE B 497 " pdb=" N PHE B 497 " pdb=" CA PHE B 497 " pdb=" CB PHE B 497 " ideal model delta harmonic sigma weight residual -122.60 -131.02 8.42 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 2643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 463 0.042 - 0.084: 140 0.084 - 0.125: 57 0.125 - 0.167: 5 0.167 - 0.209: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA PHE B 497 " pdb=" N PHE B 497 " pdb=" C PHE B 497 " pdb=" CB PHE B 497 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 664 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 165 " -0.010 2.00e-02 2.50e+03 1.19e-02 2.46e+00 pdb=" CG PHE A 165 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 165 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 165 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 165 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 165 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 165 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.011 2.00e-02 2.50e+03 8.62e-03 1.49e+00 pdb=" CG TYR B 495 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 97 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ASN A 97 " 0.019 2.00e-02 2.50e+03 pdb=" O ASN A 97 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 98 " -0.007 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 2118 2.98 - 3.46: 3801 3.46 - 3.94: 6766 3.94 - 4.42: 7776 4.42 - 4.90: 13149 Nonbonded interactions: 33610 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" N GLY A 70 " model vdw 2.495 3.120 nonbonded pdb=" OH TYR B 449 " pdb=" NH2 ARG B 498 " model vdw 2.522 3.120 nonbonded pdb=" O ASN A 97 " pdb=" OD1 ASN A 97 " model vdw 2.538 3.040 nonbonded pdb=" O SER B 446 " pdb=" NE ARG B 498 " model vdw 2.591 3.120 nonbonded pdb=" C SER B 494 " pdb=" OG SER B 494 " model vdw 2.622 2.616 ... (remaining 33605 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.010 Find NCS groups from input model: 0.030 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.003 0.032 4317 Z= 0.152 Angle : 0.590 6.907 5884 Z= 0.315 Chirality : 0.047 0.209 667 Planarity : 0.003 0.027 737 Dihedral : 14.534 83.051 1675 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.22 % Allowed : 20.88 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.36), residues: 494 helix: -3.16 (0.64), residues: 33 sheet: -0.52 (0.39), residues: 168 loop : -0.58 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.021 0.001 TYR B 495 PHE 0.027 0.001 PHE A 165 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 4303) covalent geometry : angle 0.58165 / 0.31 ( 5847) SS BOND : bond 0.00102 / 0.05 ( 5) SS BOND : angle 0.40746 / 0.27 ( 10) hydrogen bonds : bond 0.19697 / 12.48 ( 130) hydrogen bonds : angle 10.12784 / 7.10 ( 306) link_BETA1-4 : bond 0.00281 / 0.14 ( 2) link_BETA1-4 : angle 2.25328 / 1.17 ( 6) link_NAG-ASN : bond 0.00317 / 0.17 ( 7) link_NAG-ASN : angle 1.31282 / 0.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.159 Fit side-chains REVERT: A 18 LEU cc_start: 0.8911 (mm) cc_final: 0.8384 (tm) REVERT: A 141 VAL cc_start: 0.8469 (t) cc_final: 0.8216 (m) REVERT: A 153 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 403 LYS cc_start: 0.4674 (OUTLIER) cc_final: 0.4040 (mtmt) REVERT: B 406 GLU cc_start: 0.7601 (mp0) cc_final: 0.7063 (mp0) REVERT: B 452 TRP cc_start: 0.7865 (m100) cc_final: 0.7255 (m100) REVERT: B 465 GLU cc_start: 0.8294 (tt0) cc_final: 0.7925 (tt0) REVERT: B 516 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8039 (tm-30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.6947 time to fit residues: 36.5375 Evaluate side-chains 43 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0060 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.075138 restraints weight = 7979.171| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.40 r_work: 0.2997 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4317 Z= 0.145 Angle : 0.543 4.885 5884 Z= 0.284 Chirality : 0.047 0.169 667 Planarity : 0.004 0.025 737 Dihedral : 6.981 58.908 740 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.86 % Allowed : 19.78 % Favored : 77.36 % 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: -1.15 (0.36), residues: 494 helix: -2.91 (0.68), residues: 33 sheet: -0.38 (0.40), residues: 156 loop : -0.68 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 498 TYR 0.014 0.001 TYR B 495 PHE 0.020 0.001 PHE A 125 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 4303) covalent geometry : angle 0.53423 / 0.28 ( 5847) SS BOND : bond 0.00130 / 0.06 ( 5) SS BOND : angle 0.61260 / 0.38 ( 10) hydrogen bonds : bond 0.04247 / 2.79 ( 130) hydrogen bonds : angle 7.47199 / 5.33 ( 306) link_BETA1-4 : bond 0.00256 / 0.13 ( 2) link_BETA1-4 : angle 2.29325 / 1.19 ( 6) link_NAG-ASN : bond 0.00246 / 0.13 ( 7) link_NAG-ASN : angle 1.26003 / 0.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.160 Fit side-chains REVERT: A 15 VAL cc_start: 0.8552 (t) cc_final: 0.8089 (p) REVERT: A 18 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 52 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: A 141 VAL cc_start: 0.8223 (t) cc_final: 0.7814 (m) REVERT: B 403 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4433 (mtmt) REVERT: B 406 GLU cc_start: 0.7815 (mp0) cc_final: 0.7206 (mp0) REVERT: B 452 TRP cc_start: 0.7835 (m100) cc_final: 0.7284 (m100) REVERT: B 465 GLU cc_start: 0.8287 (tt0) cc_final: 0.7923 (tt0) REVERT: B 516 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8038 (tm-30) outliers start: 13 outliers final: 2 residues processed: 53 average time/residue: 0.6389 time to fit residues: 35.0068 Evaluate side-chains 46 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** A 119 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072998 restraints weight = 7945.548| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.44 r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4317 Z= 0.229 Angle : 0.583 5.221 5884 Z= 0.302 Chirality : 0.048 0.173 667 Planarity : 0.004 0.024 737 Dihedral : 7.068 57.950 740 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.52 % Allowed : 20.44 % Favored : 76.04 % 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: -1.17 (0.36), residues: 494 helix: -2.84 (0.70), residues: 33 sheet: -0.45 (0.39), residues: 167 loop : -0.66 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.016 0.002 TYR B 495 PHE 0.022 0.002 PHE A 125 TRP 0.008 0.001 TRP B 353 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 ( 4303) covalent geometry : angle 0.57167 / 0.30 ( 5847) SS BOND : bond 0.00162 / 0.08 ( 5) SS BOND : angle 0.74266 / 0.52 ( 10) hydrogen bonds : bond 0.04173 / 2.75 ( 130) hydrogen bonds : angle 7.04959 / 5.05 ( 306) link_BETA1-4 : bond 0.00117 / 0.06 ( 2) link_BETA1-4 : angle 2.31024 / 1.20 ( 6) link_NAG-ASN : bond 0.00256 / 0.15 ( 7) link_NAG-ASN : angle 1.52803 / 0.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8736 (t) cc_final: 0.8310 (p) REVERT: A 18 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 52 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8509 (tp40) REVERT: A 95 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7777 (mttm) REVERT: A 97 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (p0) REVERT: A 141 VAL cc_start: 0.8236 (t) cc_final: 0.7834 (m) REVERT: A 166 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 378 LYS cc_start: 0.7973 (mttp) cc_final: 0.7446 (mtpm) REVERT: B 403 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.4534 (mtmt) REVERT: B 406 GLU cc_start: 0.7855 (mp0) cc_final: 0.7164 (mp0) REVERT: B 465 GLU cc_start: 0.8212 (tt0) cc_final: 0.7852 (tt0) REVERT: B 516 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7962 (tm-30) outliers start: 16 outliers final: 3 residues processed: 57 average time/residue: 0.6725 time to fit residues: 39.5064 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** A 119 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.108202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074665 restraints weight = 7826.184| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.41 r_work: 0.2974 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4317 Z= 0.142 Angle : 0.542 5.671 5884 Z= 0.281 Chirality : 0.047 0.168 667 Planarity : 0.004 0.037 737 Dihedral : 6.811 57.121 740 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.86 % Allowed : 21.54 % Favored : 75.60 % 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: -1.01 (0.36), residues: 494 helix: -2.73 (0.71), residues: 33 sheet: -0.30 (0.39), residues: 166 loop : -0.58 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 357 TYR 0.012 0.001 TYR B 495 PHE 0.019 0.001 PHE A 125 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4303) covalent geometry : angle 0.53105 / 0.28 ( 5847) SS BOND : bond 0.00116 / 0.06 ( 5) SS BOND : angle 0.54538 / 0.37 ( 10) hydrogen bonds : bond 0.03568 / 2.34 ( 130) hydrogen bonds : angle 6.81395 / 4.89 ( 306) link_BETA1-4 : bond 0.00256 / 0.13 ( 2) link_BETA1-4 : angle 2.31417 / 1.20 ( 6) link_NAG-ASN : bond 0.00254 / 0.13 ( 7) link_NAG-ASN : angle 1.43202 / 0.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.205 Fit side-chains REVERT: A 15 VAL cc_start: 0.8562 (t) cc_final: 0.8097 (p) REVERT: A 18 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 52 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8504 (tp40) REVERT: A 97 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (p0) REVERT: A 141 VAL cc_start: 0.8228 (t) cc_final: 0.7827 (m) REVERT: B 378 LYS cc_start: 0.7939 (mttp) cc_final: 0.7416 (mtpm) REVERT: B 406 GLU cc_start: 0.7835 (mp0) cc_final: 0.7078 (mp0) REVERT: B 452 TRP cc_start: 0.7846 (m100) cc_final: 0.7034 (m100) REVERT: B 465 GLU cc_start: 0.8195 (tt0) cc_final: 0.7820 (tt0) REVERT: B 516 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7983 (tm-30) outliers start: 13 outliers final: 4 residues processed: 56 average time/residue: 0.6671 time to fit residues: 38.6285 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074126 restraints weight = 7884.488| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.42 r_work: 0.2959 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4317 Z= 0.179 Angle : 0.558 5.531 5884 Z= 0.289 Chirality : 0.047 0.170 667 Planarity : 0.004 0.031 737 Dihedral : 6.614 57.259 736 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.52 % Allowed : 20.44 % Favored : 76.04 % 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: -0.99 (0.36), residues: 494 helix: -2.71 (0.71), residues: 33 sheet: -0.24 (0.39), residues: 167 loop : -0.60 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.022 0.001 TYR B 495 PHE 0.020 0.001 PHE A 125 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 4303) covalent geometry : angle 0.54710 / 0.29 ( 5847) SS BOND : bond 0.00123 / 0.06 ( 5) SS BOND : angle 0.60150 / 0.43 ( 10) hydrogen bonds : bond 0.03566 / 2.35 ( 130) hydrogen bonds : angle 6.70875 / 4.81 ( 306) link_BETA1-4 : bond 0.00265 / 0.14 ( 2) link_BETA1-4 : angle 2.31609 / 1.20 ( 6) link_NAG-ASN : bond 0.00230 / 0.12 ( 7) link_NAG-ASN : angle 1.45719 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8700 (t) cc_final: 0.8271 (p) REVERT: A 18 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8500 (tt) REVERT: A 52 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8516 (tp40) REVERT: A 96 SER cc_start: 0.8883 (m) cc_final: 0.8656 (p) REVERT: A 97 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8251 (p0) REVERT: A 141 VAL cc_start: 0.8202 (t) cc_final: 0.7806 (m) REVERT: B 378 LYS cc_start: 0.7976 (mttp) cc_final: 0.7440 (mtpm) REVERT: B 406 GLU cc_start: 0.7911 (mp0) cc_final: 0.7137 (mp0) REVERT: B 465 GLU cc_start: 0.8181 (tt0) cc_final: 0.7803 (tt0) REVERT: B 516 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7982 (tm-30) outliers start: 16 outliers final: 6 residues processed: 55 average time/residue: 0.6592 time to fit residues: 37.4615 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 540 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.073877 restraints weight = 8048.062| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.40 r_work: 0.2965 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4317 Z= 0.162 Angle : 0.551 4.890 5884 Z= 0.287 Chirality : 0.047 0.170 667 Planarity : 0.003 0.031 737 Dihedral : 6.596 56.992 736 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 21.54 % Favored : 75.82 % 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: -1.00 (0.36), residues: 494 helix: -2.68 (0.71), residues: 33 sheet: -0.23 (0.39), residues: 167 loop : -0.62 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.023 0.001 TYR B 495 PHE 0.020 0.001 PHE A 125 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 4303) covalent geometry : angle 0.54057 / 0.28 ( 5847) SS BOND : bond 0.00121 / 0.06 ( 5) SS BOND : angle 0.59746 / 0.41 ( 10) hydrogen bonds : bond 0.03509 / 2.30 ( 130) hydrogen bonds : angle 6.64004 / 4.77 ( 306) link_BETA1-4 : bond 0.00205 / 0.11 ( 2) link_BETA1-4 : angle 2.31770 / 1.20 ( 6) link_NAG-ASN : bond 0.00229 / 0.12 ( 7) link_NAG-ASN : angle 1.46374 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8701 (t) cc_final: 0.8281 (p) REVERT: A 18 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 52 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: A 96 SER cc_start: 0.8926 (m) cc_final: 0.8692 (p) REVERT: A 97 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8215 (p0) REVERT: A 141 VAL cc_start: 0.8223 (t) cc_final: 0.7831 (m) REVERT: B 406 GLU cc_start: 0.7817 (mp0) cc_final: 0.7052 (mp0) REVERT: B 465 GLU cc_start: 0.8186 (tt0) cc_final: 0.7817 (tt0) REVERT: B 516 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7965 (tm-30) outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 0.6259 time to fit residues: 34.9855 Evaluate side-chains 49 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 540 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.108126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074394 restraints weight = 8016.610| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.42 r_work: 0.2975 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4317 Z= 0.128 Angle : 0.535 4.869 5884 Z= 0.278 Chirality : 0.047 0.170 667 Planarity : 0.003 0.032 737 Dihedral : 6.522 56.616 736 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.86 % Allowed : 21.98 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.36), residues: 494 helix: -2.56 (0.83), residues: 25 sheet: -0.10 (0.41), residues: 156 loop : -0.60 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.019 0.001 TYR B 495 PHE 0.019 0.001 PHE A 125 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4303) covalent geometry : angle 0.52441 / 0.28 ( 5847) SS BOND : bond 0.00101 / 0.05 ( 5) SS BOND : angle 0.48874 / 0.33 ( 10) hydrogen bonds : bond 0.03335 / 2.18 ( 130) hydrogen bonds : angle 6.52174 / 4.68 ( 306) link_BETA1-4 : bond 0.00284 / 0.14 ( 2) link_BETA1-4 : angle 2.30721 / 1.20 ( 6) link_NAG-ASN : bond 0.00243 / 0.12 ( 7) link_NAG-ASN : angle 1.43993 / 0.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.102 Fit side-chains REVERT: A 15 VAL cc_start: 0.8628 (t) cc_final: 0.8208 (p) REVERT: A 18 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8524 (tt) REVERT: A 96 SER cc_start: 0.8981 (m) cc_final: 0.8689 (p) REVERT: A 97 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8155 (p0) REVERT: A 141 VAL cc_start: 0.8208 (t) cc_final: 0.7819 (m) REVERT: A 153 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 406 GLU cc_start: 0.7809 (mp0) cc_final: 0.7057 (mp0) REVERT: B 452 TRP cc_start: 0.7904 (m100) cc_final: 0.7111 (m100) REVERT: B 465 GLU cc_start: 0.8191 (tt0) cc_final: 0.7824 (tt0) REVERT: B 516 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8009 (tm-30) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.5773 time to fit residues: 32.8154 Evaluate side-chains 49 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 193 ASN B 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074350 restraints weight = 7965.826| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.40 r_work: 0.2957 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4317 Z= 0.149 Angle : 0.560 6.425 5884 Z= 0.289 Chirality : 0.048 0.251 667 Planarity : 0.003 0.033 737 Dihedral : 6.488 56.236 736 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.20 % Allowed : 23.30 % Favored : 74.51 % 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: -0.80 (0.36), residues: 494 helix: -2.58 (0.83), residues: 25 sheet: -0.10 (0.40), residues: 166 loop : -0.55 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.019 0.001 TYR B 495 PHE 0.026 0.001 PHE A 165 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4303) covalent geometry : angle 0.54918 / 0.29 ( 5847) SS BOND : bond 0.00108 / 0.05 ( 5) SS BOND : angle 0.51869 / 0.36 ( 10) hydrogen bonds : bond 0.03346 / 2.19 ( 130) hydrogen bonds : angle 6.47762 / 4.65 ( 306) link_BETA1-4 : bond 0.00252 / 0.13 ( 2) link_BETA1-4 : angle 2.29286 / 1.19 ( 6) link_NAG-ASN : bond 0.00216 / 0.11 ( 7) link_NAG-ASN : angle 1.47037 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8684 (t) cc_final: 0.8277 (p) REVERT: A 18 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 52 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 96 SER cc_start: 0.8997 (m) cc_final: 0.8713 (p) REVERT: A 97 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8116 (p0) REVERT: A 141 VAL cc_start: 0.8211 (t) cc_final: 0.7844 (m) REVERT: A 151 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 153 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 406 GLU cc_start: 0.7841 (mp0) cc_final: 0.7045 (mp0) REVERT: B 452 TRP cc_start: 0.7904 (m100) cc_final: 0.7000 (m100) REVERT: B 465 GLU cc_start: 0.8193 (tt0) cc_final: 0.7811 (tt0) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.5895 time to fit residues: 30.9798 Evaluate side-chains 49 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073827 restraints weight = 8003.677| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.43 r_work: 0.2976 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4317 Z= 0.137 Angle : 0.554 5.064 5884 Z= 0.287 Chirality : 0.048 0.218 667 Planarity : 0.003 0.033 737 Dihedral : 6.473 56.391 736 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.20 % Allowed : 22.86 % Favored : 74.95 % 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: -0.75 (0.36), residues: 494 helix: -2.56 (0.83), residues: 25 sheet: -0.08 (0.40), residues: 166 loop : -0.50 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.019 0.001 TYR B 495 PHE 0.027 0.001 PHE A 165 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4303) covalent geometry : angle 0.54364 / 0.29 ( 5847) SS BOND : bond 0.00097 / 0.05 ( 5) SS BOND : angle 0.47664 / 0.33 ( 10) hydrogen bonds : bond 0.03293 / 2.15 ( 130) hydrogen bonds : angle 6.42410 / 4.61 ( 306) link_BETA1-4 : bond 0.00281 / 0.14 ( 2) link_BETA1-4 : angle 2.28145 / 1.19 ( 6) link_NAG-ASN : bond 0.00214 / 0.11 ( 7) link_NAG-ASN : angle 1.44856 / 0.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8693 (t) cc_final: 0.8324 (p) REVERT: A 18 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 52 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: A 96 SER cc_start: 0.9002 (m) cc_final: 0.8707 (p) REVERT: A 97 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 141 VAL cc_start: 0.8195 (t) cc_final: 0.7831 (m) REVERT: A 153 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 406 GLU cc_start: 0.7785 (mp0) cc_final: 0.6978 (mp0) REVERT: B 452 TRP cc_start: 0.7884 (m100) cc_final: 0.7077 (m100) REVERT: B 465 GLU cc_start: 0.8212 (tt0) cc_final: 0.7828 (tt0) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 0.5194 time to fit residues: 26.8108 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.073847 restraints weight = 7954.956| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.41 r_work: 0.2962 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4317 Z= 0.140 Angle : 0.567 7.268 5884 Z= 0.294 Chirality : 0.048 0.206 667 Planarity : 0.003 0.033 737 Dihedral : 6.463 55.769 736 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.20 % Allowed : 22.86 % Favored : 74.95 % 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: -0.75 (0.36), residues: 494 helix: -2.52 (0.84), residues: 25 sheet: -0.05 (0.40), residues: 165 loop : -0.52 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.019 0.001 TYR B 495 PHE 0.027 0.001 PHE A 165 TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4303) covalent geometry : angle 0.55729 / 0.29 ( 5847) SS BOND : bond 0.00097 / 0.05 ( 5) SS BOND : angle 0.47104 / 0.33 ( 10) hydrogen bonds : bond 0.03273 / 2.13 ( 130) hydrogen bonds : angle 6.38888 / 4.58 ( 306) link_BETA1-4 : bond 0.00242 / 0.12 ( 2) link_BETA1-4 : angle 2.26972 / 1.18 ( 6) link_NAG-ASN : bond 0.00210 / 0.11 ( 7) link_NAG-ASN : angle 1.43264 / 0.95 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8656 (t) cc_final: 0.8280 (p) REVERT: A 18 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 52 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: A 96 SER cc_start: 0.8969 (m) cc_final: 0.8681 (p) REVERT: A 97 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8022 (p0) REVERT: A 141 VAL cc_start: 0.8142 (t) cc_final: 0.7781 (m) REVERT: A 153 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 406 GLU cc_start: 0.7760 (mp0) cc_final: 0.6953 (mp0) REVERT: B 452 TRP cc_start: 0.7866 (m100) cc_final: 0.7096 (m100) REVERT: B 465 GLU cc_start: 0.8198 (tt0) cc_final: 0.7805 (tt0) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.5950 time to fit residues: 29.5559 Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073947 restraints weight = 7957.116| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.40 r_work: 0.2962 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4317 Z= 0.140 Angle : 0.567 6.772 5884 Z= 0.293 Chirality : 0.048 0.199 667 Planarity : 0.003 0.034 737 Dihedral : 6.451 55.797 736 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.98 % Allowed : 23.08 % Favored : 74.95 % 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: -0.73 (0.36), residues: 494 helix: -2.50 (0.84), residues: 25 sheet: -0.03 (0.40), residues: 165 loop : -0.51 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.019 0.001 TYR B 495 PHE 0.027 0.001 PHE A 165 TRP 0.005 0.001 TRP B 353 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4303) covalent geometry : angle 0.55686 / 0.29 ( 5847) SS BOND : bond 0.00095 / 0.05 ( 5) SS BOND : angle 0.46117 / 0.33 ( 10) hydrogen bonds : bond 0.03257 / 2.12 ( 130) hydrogen bonds : angle 6.36863 / 4.55 ( 306) link_BETA1-4 : bond 0.00239 / 0.12 ( 2) link_BETA1-4 : angle 2.26004 / 1.18 ( 6) link_NAG-ASN : bond 0.00202 / 0.10 ( 7) link_NAG-ASN : angle 1.43861 / 0.96 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.00 seconds wall clock time: 29 minutes 26.07 seconds (1766.07 seconds total)