Starting phenix.real_space_refine on Thu Jul 2 01:07:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upx_26677/07_2026/7upx_26677.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 20 5.16 5 C 3112 2.51 5 N 821 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1569 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.10, per 1000 atoms: 0.22 Number of scatterers: 4930 At special positions: 0 Unit cell: (96.28, 82.17, 110.39, 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 20 16.00 O 977 8.00 N 821 7.00 C 3112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 205.1 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 12.1% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.072A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.579A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.232A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY H 190 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.513A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.877A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.524A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 188 hydrogen bonds defined for protein. 456 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: 0.92 Time building geometry restraints manager: 0.54 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: 819 1.30 - 1.43: 1420 1.43 - 1.56: 2788 1.56 - 1.69: 1 1.69 - 1.82: 23 Bond restraints: 5051 Sorted by residual: bond pdb=" C TYR H 145 " pdb=" O TYR H 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" C1 FUC B 3 " pdb=" O5 FUC B 3 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CA ARG A 466 " pdb=" C ARG A 466 " ideal model delta sigma weight residual 1.520 1.566 -0.046 1.20e-02 6.94e+03 1.45e+01 bond pdb=" C6 NAG B 1 " pdb=" O6 NAG B 1 " ideal model delta sigma weight residual 1.408 1.478 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 5046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 5882 2.70 - 5.39: 936 5.39 - 8.09: 49 8.09 - 10.78: 7 10.78 - 13.48: 4 Bond angle restraints: 6878 Sorted by residual: angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.01 -13.17 1.25e+00 6.40e-01 1.11e+02 angle pdb=" N PHE H 146 " pdb=" CA PHE H 146 " pdb=" C PHE H 146 " ideal model delta sigma weight residual 109.81 123.29 -13.48 2.21e+00 2.05e-01 3.72e+01 angle pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" pdb=" CG PHE H 100G" ideal model delta sigma weight residual 113.80 119.88 -6.08 1.00e+00 1.00e+00 3.70e+01 angle pdb=" C ARG H 82B" pdb=" N LEU H 82C" pdb=" CA LEU H 82C" ideal model delta sigma weight residual 121.05 129.71 -8.66 1.43e+00 4.89e-01 3.67e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 ... (remaining 6873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 2719 17.12 - 34.24: 186 34.24 - 51.36: 38 51.36 - 68.47: 12 68.47 - 85.59: 7 Dihedral angle restraints: 2962 sinusoidal: 1123 harmonic: 1839 Sorted by residual: dihedral pdb=" C TYR A 495 " pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta harmonic sigma weight residual -122.60 -108.66 -13.94 0 2.50e+00 1.60e-01 3.11e+01 dihedral pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CA TYR L 140 " pdb=" CB TYR L 140 " ideal model delta harmonic sigma weight residual 122.80 135.52 -12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 595 0.120 - 0.239: 147 0.239 - 0.358: 22 0.358 - 0.477: 4 0.477 - 0.596: 1 Chirality restraints: 769 Sorted by residual: chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.22e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" CA TYR L 140 " pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CB TYR L 140 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 766 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.100 2.00e-02 2.50e+03 5.75e-02 6.62e+01 pdb=" CG TYR L 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 90 " -0.075 2.00e-02 2.50e+03 4.78e-02 4.58e+01 pdb=" CG TYR H 90 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 90 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 90 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR H 90 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 90 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 91 " 0.093 2.00e-02 2.50e+03 4.74e-02 4.50e+01 pdb=" CG TYR L 91 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR L 91 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR L 91 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 91 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 91 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 91 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR L 91 " 0.034 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 118 2.72 - 3.27: 4640 3.27 - 3.81: 7348 3.81 - 4.36: 10325 4.36 - 4.90: 16877 Nonbonded interactions: 39308 Sorted by model distance: nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 140 " model vdw 2.176 3.040 nonbonded pdb=" CB GLU H 148 " pdb=" CD PRO H 149 " model vdw 2.190 3.840 nonbonded pdb=" OD1 ASP A 442 " pdb=" OG SER H 100B" model vdw 2.297 3.040 nonbonded pdb=" O ARG L 142 " pdb=" N ALA L 144 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS H 209 " pdb=" OE1 GLU L 123 " model vdw 2.429 3.120 ... (remaining 39303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.260 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: 0.020 Set scattering table: 0.000 Process input model: 6.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 : 0.013 0.081 5058 Z= 0.736 Angle : 1.883 13.479 6895 Z= 1.230 Chirality : 0.106 0.596 769 Planarity : 0.012 0.120 885 Dihedral : 13.520 85.594 1778 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.43 % Allowed : 5.41 % Favored : 93.16 % Rotamer: Outliers : 2.20 % Allowed : 4.77 % Favored : 93.03 % Cbeta Deviations : 0.68 % 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: -0.66 (0.32), residues: 629 helix: -3.80 (0.43), residues: 46 sheet: 0.50 (0.33), residues: 235 loop : -0.57 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100A TYR 0.100 0.016 TYR L 32 PHE 0.063 0.014 PHE H 100G TRP 0.063 0.016 TRP L 35 HIS 0.010 0.004 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.01269 / 0.74 ( 5051) covalent geometry : angle 1.87749 / 1.23 ( 6878) SS BOND : bond 0.00850 / 0.40 ( 4) SS BOND : angle 1.23476 / 0.59 ( 8) hydrogen bonds : bond 0.14921 / 9.87 ( 173) hydrogen bonds : angle 8.87402 / 6.14 ( 456) link_BETA1-4 : bond 0.02569 / 1.35 ( 1) link_BETA1-4 : angle 4.15115 / 2.15 ( 3) link_BETA1-6 : bond 0.03602 / 1.90 ( 1) link_BETA1-6 : angle 5.37931 / 2.62 ( 3) link_NAG-ASN : bond 0.00971 / 0.51 ( 1) link_NAG-ASN : angle 4.52525 / 2.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.216 Fit side-chains REVERT: A 443 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8640 (p) REVERT: H 148 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5282 (tt0) REVERT: L 48 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8753 (mp) REVERT: L 103 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8838 (mtpp) REVERT: L 188 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8533 (pttm) outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.1002 time to fit residues: 13.3646 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106766 restraints weight = 6359.776| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.42 r_work: 0.3090 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5058 Z= 0.169 Angle : 0.728 10.110 6895 Z= 0.377 Chirality : 0.049 0.188 769 Planarity : 0.005 0.039 885 Dihedral : 7.729 84.886 703 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.50 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 9.54 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.03 (0.34), residues: 629 helix: -2.86 (0.58), residues: 46 sheet: 0.78 (0.32), residues: 265 loop : -0.19 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 108 TYR 0.025 0.002 TYR L 91 PHE 0.034 0.002 PHE H 146 TRP 0.021 0.002 TRP H 50 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 5051) covalent geometry : angle 0.72743 / 0.38 ( 6878) SS BOND : bond 0.00435 / 0.19 ( 4) SS BOND : angle 0.79045 / 0.37 ( 8) hydrogen bonds : bond 0.03877 / 2.54 ( 173) hydrogen bonds : angle 6.44892 / 4.36 ( 456) link_BETA1-4 : bond 0.00087 / 0.05 ( 1) link_BETA1-4 : angle 1.17494 / 0.55 ( 3) link_BETA1-6 : bond 0.00740 / 0.39 ( 1) link_BETA1-6 : angle 1.38544 / 0.59 ( 3) link_NAG-ASN : bond 0.00279 / 0.15 ( 1) link_NAG-ASN : angle 0.93419 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.144 Fit side-chains REVERT: A 340 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8038 (mm-30) REVERT: A 440 ASN cc_start: 0.8514 (p0) cc_final: 0.8040 (t0) REVERT: A 443 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8835 (p) REVERT: H 209 LYS cc_start: 0.6764 (tppt) cc_final: 0.6495 (mmtt) REVERT: L 167 ASP cc_start: 0.8051 (t0) cc_final: 0.7604 (t0) REVERT: L 183 LYS cc_start: 0.8299 (tptm) cc_final: 0.7767 (tptp) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.0969 time to fit residues: 11.8138 Evaluate side-chains 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105126 restraints weight = 6378.136| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.40 r_work: 0.3060 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5058 Z= 0.196 Angle : 0.698 9.032 6895 Z= 0.354 Chirality : 0.048 0.168 769 Planarity : 0.005 0.033 885 Dihedral : 5.896 47.871 694 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.25 % Favored : 94.44 % Rotamer: Outliers : 2.39 % Allowed : 11.56 % Favored : 86.06 % 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: 0.09 (0.34), residues: 629 helix: -2.30 (0.65), residues: 46 sheet: 0.88 (0.33), residues: 256 loop : -0.18 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 108 TYR 0.023 0.002 TYR L 91 PHE 0.014 0.002 PHE L 71 TRP 0.018 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 5051) covalent geometry : angle 0.69683 / 0.35 ( 6878) SS BOND : bond 0.00412 / 0.19 ( 4) SS BOND : angle 0.80632 / 0.39 ( 8) hydrogen bonds : bond 0.03475 / 2.24 ( 173) hydrogen bonds : angle 5.94765 / 4.01 ( 456) link_BETA1-4 : bond 0.00255 / 0.13 ( 1) link_BETA1-4 : angle 1.26502 / 0.60 ( 3) link_BETA1-6 : bond 0.00926 / 0.49 ( 1) link_BETA1-6 : angle 1.27776 / 0.57 ( 3) link_NAG-ASN : bond 0.00127 / 0.07 ( 1) link_NAG-ASN : angle 1.46014 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.113 Fit side-chains REVERT: A 340 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8025 (mm-30) REVERT: A 440 ASN cc_start: 0.8473 (p0) cc_final: 0.8060 (t0) REVERT: A 466 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7811 (ptp90) REVERT: H 148 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6243 (tp30) REVERT: H 209 LYS cc_start: 0.6878 (tppt) cc_final: 0.6610 (mmtt) REVERT: L 167 ASP cc_start: 0.7969 (t0) cc_final: 0.7410 (t0) REVERT: L 183 LYS cc_start: 0.8327 (tptm) cc_final: 0.7791 (tptp) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.0740 time to fit residues: 7.8926 Evaluate side-chains 76 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 422 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 = 0.3724 r_free = 0.3724 target = 0.147456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109202 restraints weight = 6307.294| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.29 r_work: 0.3073 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5058 Z= 0.160 Angle : 0.651 7.999 6895 Z= 0.329 Chirality : 0.046 0.140 769 Planarity : 0.004 0.032 885 Dihedral : 5.615 48.088 692 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.66 % Favored : 96.03 % Rotamer: Outliers : 2.39 % Allowed : 12.66 % Favored : 84.95 % 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: 0.20 (0.34), residues: 629 helix: -1.65 (0.74), residues: 40 sheet: 0.84 (0.33), residues: 260 loop : -0.14 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 108 TYR 0.021 0.002 TYR L 91 PHE 0.016 0.001 PHE H 146 TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5051) covalent geometry : angle 0.64966 / 0.33 ( 6878) SS BOND : bond 0.00357 / 0.16 ( 4) SS BOND : angle 0.67282 / 0.32 ( 8) hydrogen bonds : bond 0.03118 / 1.99 ( 173) hydrogen bonds : angle 5.70826 / 3.85 ( 456) link_BETA1-4 : bond 0.00190 / 0.10 ( 1) link_BETA1-4 : angle 1.23442 / 0.58 ( 3) link_BETA1-6 : bond 0.00710 / 0.37 ( 1) link_BETA1-6 : angle 1.18678 / 0.51 ( 3) link_NAG-ASN : bond 0.00043 / 0.02 ( 1) link_NAG-ASN : angle 1.42143 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.113 Fit side-chains REVERT: A 440 ASN cc_start: 0.8371 (p0) cc_final: 0.7922 (t0) REVERT: A 466 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7730 (ptp90) REVERT: H 148 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6465 (tp30) REVERT: H 209 LYS cc_start: 0.6970 (tppt) cc_final: 0.6726 (tptp) REVERT: L 149 LYS cc_start: 0.6148 (mtmt) cc_final: 0.5928 (mtmt) REVERT: L 167 ASP cc_start: 0.7972 (t0) cc_final: 0.7394 (t0) REVERT: L 183 LYS cc_start: 0.8313 (tptm) cc_final: 0.7657 (tptp) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.0846 time to fit residues: 8.4438 Evaluate side-chains 77 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104549 restraints weight = 6414.478| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.32 r_work: 0.2959 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 5058 Z= 0.320 Angle : 0.764 9.393 6895 Z= 0.384 Chirality : 0.050 0.166 769 Planarity : 0.005 0.033 885 Dihedral : 5.906 50.745 692 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.77 % Favored : 94.91 % Rotamer: Outliers : 3.12 % Allowed : 13.58 % Favored : 83.30 % 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: -0.16 (0.34), residues: 629 helix: -1.84 (0.71), residues: 46 sheet: 0.74 (0.33), residues: 260 loop : -0.50 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 108 TYR 0.024 0.003 TYR L 91 PHE 0.021 0.002 PHE L 71 TRP 0.018 0.003 TRP H 36 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.32 ( 5051) covalent geometry : angle 0.76201 / 0.38 ( 6878) SS BOND : bond 0.00411 / 0.18 ( 4) SS BOND : angle 0.82905 / 0.40 ( 8) hydrogen bonds : bond 0.03648 / 2.34 ( 173) hydrogen bonds : angle 5.93500 / 4.03 ( 456) link_BETA1-4 : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : angle 1.51169 / 0.70 ( 3) link_BETA1-6 : bond 0.00717 / 0.38 ( 1) link_BETA1-6 : angle 1.39390 / 0.58 ( 3) link_NAG-ASN : bond 0.00492 / 0.26 ( 1) link_NAG-ASN : angle 1.90218 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.120 Fit side-chains REVERT: A 440 ASN cc_start: 0.8402 (p0) cc_final: 0.8062 (t0) REVERT: A 466 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8104 (ptp90) REVERT: H 148 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: H 209 LYS cc_start: 0.6947 (tppt) cc_final: 0.6478 (mmtt) REVERT: L 167 ASP cc_start: 0.7859 (t0) cc_final: 0.7077 (m-30) REVERT: L 183 LYS cc_start: 0.8379 (tptm) cc_final: 0.7694 (tptp) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.0711 time to fit residues: 6.9654 Evaluate side-chains 77 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108033 restraints weight = 6440.295| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.34 r_work: 0.3053 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5058 Z= 0.171 Angle : 0.650 7.768 6895 Z= 0.327 Chirality : 0.046 0.139 769 Planarity : 0.004 0.034 885 Dihedral : 5.683 51.764 692 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.66 % Favored : 96.03 % Rotamer: Outliers : 2.94 % Allowed : 14.31 % Favored : 82.75 % 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: -0.05 (0.34), residues: 629 helix: -1.72 (0.73), residues: 46 sheet: 0.83 (0.32), residues: 265 loop : -0.47 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 108 TYR 0.020 0.002 TYR L 91 PHE 0.013 0.001 PHE H 146 TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 5051) covalent geometry : angle 0.64834 / 0.33 ( 6878) SS BOND : bond 0.00324 / 0.15 ( 4) SS BOND : angle 0.73462 / 0.33 ( 8) hydrogen bonds : bond 0.03077 / 1.97 ( 173) hydrogen bonds : angle 5.61138 / 3.84 ( 456) link_BETA1-4 : bond 0.00244 / 0.13 ( 1) link_BETA1-4 : angle 1.36637 / 0.62 ( 3) link_BETA1-6 : bond 0.00818 / 0.43 ( 1) link_BETA1-6 : angle 1.26062 / 0.54 ( 3) link_NAG-ASN : bond 0.00120 / 0.06 ( 1) link_NAG-ASN : angle 1.55579 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.136 Fit side-chains REVERT: A 440 ASN cc_start: 0.8403 (p0) cc_final: 0.7993 (t0) REVERT: A 466 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.7678 (ptp90) REVERT: H 148 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6487 (tp30) REVERT: H 209 LYS cc_start: 0.6910 (tppt) cc_final: 0.6497 (mmtt) REVERT: L 29 ILE cc_start: 0.8611 (mm) cc_final: 0.8342 (mm) REVERT: L 149 LYS cc_start: 0.6373 (mtmt) cc_final: 0.6138 (mtmt) REVERT: L 167 ASP cc_start: 0.7928 (t0) cc_final: 0.7188 (m-30) REVERT: L 183 LYS cc_start: 0.8357 (tptm) cc_final: 0.7688 (tptp) REVERT: L 199 GLN cc_start: 0.8628 (tt0) cc_final: 0.8140 (mt0) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0949 time to fit residues: 9.3564 Evaluate side-chains 81 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106411 restraints weight = 6309.622| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.43 r_work: 0.3082 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5058 Z= 0.145 Angle : 0.621 7.076 6895 Z= 0.311 Chirality : 0.045 0.135 769 Planarity : 0.004 0.034 885 Dihedral : 5.467 51.870 692 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 2.94 % Allowed : 14.50 % Favored : 82.57 % 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: 0.29 (0.35), residues: 629 helix: -0.95 (0.85), residues: 40 sheet: 0.90 (0.32), residues: 265 loop : -0.20 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 108 TYR 0.019 0.002 TYR L 91 PHE 0.012 0.001 PHE H 146 TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 5051) covalent geometry : angle 0.62010 / 0.31 ( 6878) SS BOND : bond 0.00296 / 0.14 ( 4) SS BOND : angle 0.54504 / 0.24 ( 8) hydrogen bonds : bond 0.02856 / 1.82 ( 173) hydrogen bonds : angle 5.35411 / 3.68 ( 456) link_BETA1-4 : bond 0.00267 / 0.14 ( 1) link_BETA1-4 : angle 1.28489 / 0.58 ( 3) link_BETA1-6 : bond 0.00742 / 0.39 ( 1) link_BETA1-6 : angle 1.25409 / 0.53 ( 3) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.44577 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.189 Fit side-chains REVERT: A 440 ASN cc_start: 0.8400 (p0) cc_final: 0.7920 (t0) REVERT: A 466 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.7519 (ptp90) REVERT: A 487 ASN cc_start: 0.7887 (m-40) cc_final: 0.7627 (m-40) REVERT: H 148 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: H 209 LYS cc_start: 0.6923 (tppt) cc_final: 0.6531 (mmtt) REVERT: L 29 ILE cc_start: 0.8572 (mm) cc_final: 0.8321 (mm) REVERT: L 149 LYS cc_start: 0.6500 (mtmt) cc_final: 0.6225 (mtmt) REVERT: L 167 ASP cc_start: 0.7903 (t0) cc_final: 0.7229 (m-30) REVERT: L 183 LYS cc_start: 0.8329 (tptm) cc_final: 0.7679 (tptp) REVERT: L 199 GLN cc_start: 0.8596 (tt0) cc_final: 0.8152 (mt0) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.0958 time to fit residues: 9.5465 Evaluate side-chains 79 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108976 restraints weight = 6404.841| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.33 r_work: 0.3057 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5058 Z= 0.142 Angle : 0.619 6.813 6895 Z= 0.309 Chirality : 0.045 0.137 769 Planarity : 0.004 0.032 885 Dihedral : 5.404 52.501 692 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 2.75 % Allowed : 14.68 % Favored : 82.57 % 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: 0.30 (0.34), residues: 629 helix: -0.94 (0.84), residues: 40 sheet: 1.02 (0.33), residues: 255 loop : -0.26 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 108 TYR 0.020 0.002 TYR L 91 PHE 0.010 0.001 PHE H 166 TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5051) covalent geometry : angle 0.61766 / 0.31 ( 6878) SS BOND : bond 0.00313 / 0.15 ( 4) SS BOND : angle 0.50744 / 0.23 ( 8) hydrogen bonds : bond 0.02791 / 1.77 ( 173) hydrogen bonds : angle 5.24656 / 3.60 ( 456) link_BETA1-4 : bond 0.00314 / 0.17 ( 1) link_BETA1-4 : angle 1.29140 / 0.58 ( 3) link_BETA1-6 : bond 0.00716 / 0.38 ( 1) link_BETA1-6 : angle 1.24949 / 0.52 ( 3) link_NAG-ASN : bond 0.00060 / 0.03 ( 1) link_NAG-ASN : angle 1.48639 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.189 Fit side-chains REVERT: A 438 SER cc_start: 0.9205 (m) cc_final: 0.8689 (t) REVERT: A 440 ASN cc_start: 0.8403 (p0) cc_final: 0.7953 (t0) REVERT: A 487 ASN cc_start: 0.7885 (m-40) cc_final: 0.7613 (m-40) REVERT: H 117 LYS cc_start: 0.8095 (tttt) cc_final: 0.7624 (tttp) REVERT: H 209 LYS cc_start: 0.6926 (tppt) cc_final: 0.6546 (mmtt) REVERT: L 29 ILE cc_start: 0.8554 (mm) cc_final: 0.8298 (mm) REVERT: L 149 LYS cc_start: 0.6507 (mtmt) cc_final: 0.6218 (mtmt) REVERT: L 167 ASP cc_start: 0.7907 (t0) cc_final: 0.7282 (m-30) REVERT: L 183 LYS cc_start: 0.8335 (tptm) cc_final: 0.7712 (tptp) REVERT: L 199 GLN cc_start: 0.8604 (tt0) cc_final: 0.8223 (mt0) outliers start: 15 outliers final: 14 residues processed: 82 average time/residue: 0.0987 time to fit residues: 10.0339 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110642 restraints weight = 6236.266| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.45 r_work: 0.3119 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5058 Z= 0.097 Angle : 0.581 6.914 6895 Z= 0.289 Chirality : 0.044 0.148 769 Planarity : 0.004 0.031 885 Dihedral : 5.192 53.169 692 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 2.02 % Allowed : 15.41 % Favored : 82.57 % 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: 0.42 (0.34), residues: 629 helix: -0.74 (0.85), residues: 40 sheet: 1.07 (0.32), residues: 255 loop : -0.16 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.014 0.001 TYR L 91 PHE 0.007 0.001 PHE H 166 TRP 0.017 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 5051) covalent geometry : angle 0.57993 / 0.29 ( 6878) SS BOND : bond 0.00297 / 0.14 ( 4) SS BOND : angle 0.43042 / 0.19 ( 8) hydrogen bonds : bond 0.02533 / 1.61 ( 173) hydrogen bonds : angle 4.97371 / 3.42 ( 456) link_BETA1-4 : bond 0.00436 / 0.23 ( 1) link_BETA1-4 : angle 1.14321 / 0.51 ( 3) link_BETA1-6 : bond 0.00782 / 0.41 ( 1) link_BETA1-6 : angle 1.15455 / 0.49 ( 3) link_NAG-ASN : bond 0.00204 / 0.11 ( 1) link_NAG-ASN : angle 1.19003 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.203 Fit side-chains REVERT: A 438 SER cc_start: 0.9146 (m) cc_final: 0.8889 (p) REVERT: A 440 ASN cc_start: 0.8386 (p0) cc_final: 0.7937 (t0) REVERT: A 487 ASN cc_start: 0.7924 (m-40) cc_final: 0.7678 (m-40) REVERT: H 117 LYS cc_start: 0.8066 (tttt) cc_final: 0.7593 (tttp) REVERT: L 29 ILE cc_start: 0.8513 (mm) cc_final: 0.8267 (mm) REVERT: L 31 ASP cc_start: 0.8209 (p0) cc_final: 0.7941 (p0) REVERT: L 149 LYS cc_start: 0.6564 (mtmt) cc_final: 0.6273 (mtmt) REVERT: L 167 ASP cc_start: 0.7922 (t0) cc_final: 0.7283 (m-30) REVERT: L 183 LYS cc_start: 0.8318 (tptm) cc_final: 0.7678 (tptp) REVERT: L 199 GLN cc_start: 0.8531 (tt0) cc_final: 0.8188 (mt0) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0920 time to fit residues: 10.2344 Evaluate side-chains 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107417 restraints weight = 6328.068| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.48 r_work: 0.3084 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5058 Z= 0.153 Angle : 0.628 6.746 6895 Z= 0.313 Chirality : 0.045 0.133 769 Planarity : 0.004 0.031 885 Dihedral : 5.266 54.242 692 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 16.51 % Favored : 81.47 % 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: 0.22 (0.34), residues: 629 helix: -1.48 (0.75), residues: 46 sheet: 1.05 (0.33), residues: 255 loop : -0.30 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.021 0.002 TYR L 91 PHE 0.011 0.001 PHE H 122 TRP 0.016 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5051) covalent geometry : angle 0.62651 / 0.31 ( 6878) SS BOND : bond 0.00355 / 0.17 ( 4) SS BOND : angle 0.50338 / 0.25 ( 8) hydrogen bonds : bond 0.02729 / 1.73 ( 173) hydrogen bonds : angle 5.06390 / 3.49 ( 456) link_BETA1-4 : bond 0.00226 / 0.12 ( 1) link_BETA1-4 : angle 1.19037 / 0.55 ( 3) link_BETA1-6 : bond 0.00902 / 0.47 ( 1) link_BETA1-6 : angle 1.27460 / 0.52 ( 3) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 1.47255 / 0.63 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.197 Fit side-chains REVERT: A 438 SER cc_start: 0.9181 (m) cc_final: 0.8754 (t) REVERT: A 440 ASN cc_start: 0.8480 (p0) cc_final: 0.8025 (t0) REVERT: A 466 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8341 (ptp90) REVERT: A 487 ASN cc_start: 0.7932 (m-40) cc_final: 0.7685 (m-40) REVERT: H 117 LYS cc_start: 0.8076 (tttt) cc_final: 0.7608 (tttp) REVERT: H 209 LYS cc_start: 0.7086 (tptp) cc_final: 0.6819 (mmtt) REVERT: L 29 ILE cc_start: 0.8556 (mm) cc_final: 0.8312 (mm) REVERT: L 149 LYS cc_start: 0.6580 (mtmt) cc_final: 0.6284 (mtmt) REVERT: L 167 ASP cc_start: 0.7905 (t0) cc_final: 0.7281 (m-30) REVERT: L 183 LYS cc_start: 0.8300 (tptm) cc_final: 0.7654 (tptp) REVERT: L 199 GLN cc_start: 0.8571 (tt0) cc_final: 0.8186 (mt0) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.0961 time to fit residues: 9.8296 Evaluate side-chains 85 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105462 restraints weight = 6343.377| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.45 r_work: 0.3028 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5058 Z= 0.191 Angle : 0.651 7.235 6895 Z= 0.323 Chirality : 0.046 0.139 769 Planarity : 0.004 0.031 885 Dihedral : 5.397 55.549 692 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 1.65 % Allowed : 17.06 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.34), residues: 629 helix: -1.50 (0.76), residues: 46 sheet: 0.96 (0.33), residues: 255 loop : -0.32 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100A TYR 0.021 0.002 TYR L 91 PHE 0.012 0.002 PHE L 71 TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 5051) covalent geometry : angle 0.64988 / 0.32 ( 6878) SS BOND : bond 0.00335 / 0.15 ( 4) SS BOND : angle 0.57285 / 0.28 ( 8) hydrogen bonds : bond 0.02938 / 1.88 ( 173) hydrogen bonds : angle 5.16879 / 3.56 ( 456) link_BETA1-4 : bond 0.00193 / 0.10 ( 1) link_BETA1-4 : angle 1.21999 / 0.56 ( 3) link_BETA1-6 : bond 0.00778 / 0.41 ( 1) link_BETA1-6 : angle 1.23398 / 0.51 ( 3) link_NAG-ASN : bond 0.00179 / 0.09 ( 1) link_NAG-ASN : angle 1.61931 / 0.66 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.67 seconds wall clock time: 28 minutes 2.44 seconds (1682.44 seconds total)