Starting phenix.real_space_refine on Thu Mar 6 05:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_26677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_26677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_26677.map" model { file = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_26677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2025/7upx_26677.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.58, per 1000 atoms: 1.13 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: 1.15 Conformation dependent library (CDL) restraints added in 553.1 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: 0.61 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: 1.54 Time building geometry restraints manager: 1.37 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 - 22.86: 2868 22.86 - 45.72: 119 45.72 - 68.57: 20 68.57 - 91.43: 12 91.43 - 114.29: 2 Dihedral angle restraints: 3021 sinusoidal: 1182 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 3018 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: 152.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.820 Find NCS groups from input model: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 5051 Z= 0.820 Angle : 1.877 13.479 6878 Z= 1.230 Chirality : 0.106 0.596 769 Planarity : 0.012 0.120 885 Dihedral : 14.710 114.291 1837 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (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 TRP 0.063 0.016 TRP L 35 HIS 0.010 0.004 HIS L 198 PHE 0.063 0.014 PHE H 100G TYR 0.100 0.016 TYR L 32 ARG 0.007 0.001 ARG H 100A *********************** 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 : 0.611 Fit side-chains REVERT: A 443 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8639 (p) REVERT: H 148 GLU cc_start: 0.6399 (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: 0.8860 (ptmm) cc_final: 0.8533 (pttm) outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.3070 time to fit residues: 40.5397 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 : 0.581 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN L 199 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 = 0.147758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106220 restraints weight = 6259.128| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.38 r_work: 0.3081 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5051 Z= 0.280 Angle : 0.749 10.482 6878 Z= 0.387 Chirality : 0.050 0.189 769 Planarity : 0.005 0.040 885 Dihedral : 10.414 93.133 762 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.34 % Favored : 96.18 % Rotamer: Outliers : 1.83 % Allowed : 9.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.34), residues: 629 helix: -2.91 (0.57), residues: 46 sheet: 0.78 (0.32), residues: 265 loop : -0.22 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 50 HIS 0.005 0.002 HIS H 200 PHE 0.034 0.002 PHE H 146 TYR 0.026 0.002 TYR L 91 ARG 0.004 0.001 ARG L 108 *********************** 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 104 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.550 Fit side-chains REVERT: A 340 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8045 (mm-30) REVERT: A 440 ASN cc_start: 0.8517 (p0) cc_final: 0.8037 (t0) REVERT: A 443 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (p) REVERT: H 209 LYS cc_start: 0.6757 (tppt) cc_final: 0.6498 (mmtt) REVERT: L 48 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8509 (mp) REVERT: L 167 ASP cc_start: 0.8052 (t0) cc_final: 0.7602 (t0) REVERT: L 183 LYS cc_start: 0.8291 (tptm) cc_final: 0.7761 (tptp) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.2719 time to fit residues: 33.4637 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 48 ILE 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 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3729 r_free = 0.3729 target = 0.148074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106459 restraints weight = 6339.899| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.41 r_work: 0.3082 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5051 Z= 0.244 Angle : 0.683 9.323 6878 Z= 0.344 Chirality : 0.047 0.181 769 Planarity : 0.005 0.033 885 Dihedral : 7.993 72.543 755 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.09 % Favored : 94.59 % Rotamer: Outliers : 2.20 % Allowed : 11.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.34), residues: 629 helix: -2.29 (0.65), residues: 46 sheet: 0.91 (0.33), residues: 262 loop : -0.17 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE H 146 TYR 0.021 0.002 TYR L 91 ARG 0.003 0.000 ARG L 108 *********************** 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 91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.633 Fit side-chains REVERT: A 340 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8000 (mm-30) REVERT: A 440 ASN cc_start: 0.8463 (p0) cc_final: 0.8049 (t0) REVERT: H 148 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: H 209 LYS cc_start: 0.6854 (tppt) cc_final: 0.6589 (mmtt) REVERT: L 31 ASP cc_start: 0.8332 (p0) cc_final: 0.8094 (p0) REVERT: L 55 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: L 167 ASP cc_start: 0.7960 (t0) cc_final: 0.7442 (t0) REVERT: L 183 LYS cc_start: 0.8319 (tptm) cc_final: 0.7682 (tptp) outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 0.2246 time to fit residues: 25.0295 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN 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 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN L 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107005 restraints weight = 6375.939| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.40 r_work: 0.3086 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5051 Z= 0.230 Angle : 0.652 7.754 6878 Z= 0.326 Chirality : 0.046 0.164 769 Planarity : 0.004 0.032 885 Dihedral : 7.033 59.029 751 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.82 % Favored : 95.87 % Rotamer: Outliers : 2.02 % Allowed : 12.48 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.34), residues: 629 helix: -1.52 (0.75), residues: 40 sheet: 0.89 (0.33), residues: 258 loop : -0.04 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 146 TYR 0.021 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** 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 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.897 Fit side-chains REVERT: A 440 ASN cc_start: 0.8315 (p0) cc_final: 0.7882 (t0) REVERT: A 466 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7392 (ptp90) REVERT: H 148 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: H 209 LYS cc_start: 0.6948 (tppt) cc_final: 0.6710 (tptp) REVERT: L 55 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: L 167 ASP cc_start: 0.7974 (t0) cc_final: 0.7462 (t0) REVERT: L 183 LYS cc_start: 0.8341 (tptm) cc_final: 0.7663 (tptp) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.3638 time to fit residues: 35.9596 Evaluate side-chains 78 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.145701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103906 restraints weight = 6288.508| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.43 r_work: 0.3047 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5051 Z= 0.372 Angle : 0.710 8.471 6878 Z= 0.352 Chirality : 0.048 0.163 769 Planarity : 0.004 0.032 885 Dihedral : 6.839 51.767 751 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.39 % Rotamer: Outliers : 2.57 % Allowed : 13.58 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.35), residues: 629 helix: -1.26 (0.82), residues: 40 sheet: 0.85 (0.33), residues: 260 loop : -0.11 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.004 0.002 HIS H 35 PHE 0.016 0.002 PHE L 71 TYR 0.023 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** 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 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.825 Fit side-chains REVERT: A 440 ASN cc_start: 0.8464 (p0) cc_final: 0.8072 (t0) REVERT: A 466 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8000 (ptp90) REVERT: H 148 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: H 209 LYS cc_start: 0.7013 (tppt) cc_final: 0.6799 (tptp) REVERT: L 167 ASP cc_start: 0.7955 (t0) cc_final: 0.7407 (t0) REVERT: L 183 LYS cc_start: 0.8370 (tptm) cc_final: 0.7706 (tptp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.3188 time to fit residues: 32.4767 Evaluate side-chains 78 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 56 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3724 r_free = 0.3724 target = 0.147626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106240 restraints weight = 6291.876| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.38 r_work: 0.3079 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5051 Z= 0.238 Angle : 0.648 7.471 6878 Z= 0.322 Chirality : 0.046 0.147 769 Planarity : 0.004 0.033 885 Dihedral : 6.451 50.354 751 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.66 % Favored : 96.03 % Rotamer: Outliers : 2.75 % Allowed : 13.76 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.35), residues: 629 helix: -1.18 (0.83), residues: 40 sheet: 0.91 (0.33), residues: 260 loop : -0.08 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE H 146 TYR 0.020 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** 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 81 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.530 Fit side-chains REVERT: A 440 ASN cc_start: 0.8328 (p0) cc_final: 0.7874 (t0) REVERT: A 466 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7858 (ptp90) REVERT: H 148 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: L 29 ILE cc_start: 0.8587 (mm) cc_final: 0.8343 (mm) REVERT: L 55 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: L 167 ASP cc_start: 0.7962 (t0) cc_final: 0.7317 (m-30) REVERT: L 183 LYS cc_start: 0.8387 (tptm) cc_final: 0.7713 (tptp) REVERT: L 199 GLN cc_start: 0.8626 (tt0) cc_final: 0.8150 (mt0) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.2383 time to fit residues: 22.3013 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 : 0.528 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3726 r_free = 0.3726 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106427 restraints weight = 6272.271| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.43 r_work: 0.3082 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5051 Z= 0.247 Angle : 0.645 7.308 6878 Z= 0.319 Chirality : 0.046 0.134 769 Planarity : 0.004 0.032 885 Dihedral : 6.243 51.276 751 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 2.75 % Allowed : 13.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.35), residues: 629 helix: -1.15 (0.84), residues: 40 sheet: 0.97 (0.32), residues: 265 loop : -0.09 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE L 71 TYR 0.022 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 *********************** 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 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.717 Fit side-chains REVERT: A 440 ASN cc_start: 0.8367 (p0) cc_final: 0.7910 (t0) REVERT: A 466 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.7971 (ptp90) REVERT: H 148 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: H 209 LYS cc_start: 0.7081 (tptp) cc_final: 0.6783 (mmtt) REVERT: L 29 ILE cc_start: 0.8586 (mm) cc_final: 0.8325 (mm) REVERT: L 55 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: L 167 ASP cc_start: 0.7955 (t0) cc_final: 0.7287 (m-30) REVERT: L 183 LYS cc_start: 0.8368 (tptm) cc_final: 0.7699 (tptp) REVERT: L 199 GLN cc_start: 0.8610 (tt0) cc_final: 0.8177 (mt0) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.3285 time to fit residues: 31.9025 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 146 VAL 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 49 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3716 r_free = 0.3716 target = 0.146920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105455 restraints weight = 6285.552| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.41 r_work: 0.3071 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5051 Z= 0.289 Angle : 0.664 7.533 6878 Z= 0.328 Chirality : 0.046 0.138 769 Planarity : 0.004 0.031 885 Dihedral : 6.215 52.552 751 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 3.49 % Allowed : 13.39 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.35), residues: 629 helix: -1.27 (0.81), residues: 40 sheet: 0.95 (0.32), residues: 265 loop : -0.14 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE L 71 TYR 0.026 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 *********************** 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 87 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.585 Fit side-chains REVERT: A 440 ASN cc_start: 0.8395 (p0) cc_final: 0.7967 (t0) REVERT: A 466 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8050 (ptp90) REVERT: H 148 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: H 209 LYS cc_start: 0.7132 (tptp) cc_final: 0.6837 (mmtt) REVERT: L 29 ILE cc_start: 0.8595 (mm) cc_final: 0.8368 (mm) REVERT: L 55 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: L 167 ASP cc_start: 0.7945 (t0) cc_final: 0.7286 (m-30) REVERT: L 183 LYS cc_start: 0.8368 (tptm) cc_final: 0.7698 (tptp) REVERT: L 199 GLN cc_start: 0.8610 (tt0) cc_final: 0.8236 (mt0) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.2921 time to fit residues: 29.0522 Evaluate side-chains 85 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 178 LEU 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 124 GLN 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 13 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3737 r_free = 0.3737 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107197 restraints weight = 6264.924| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.42 r_work: 0.3095 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5051 Z= 0.204 Angle : 0.632 7.118 6878 Z= 0.312 Chirality : 0.045 0.139 769 Planarity : 0.004 0.031 885 Dihedral : 6.071 52.956 751 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.35), residues: 629 helix: -1.24 (0.81), residues: 40 sheet: 1.05 (0.33), residues: 255 loop : -0.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 59 TYR 0.024 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 *********************** 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 90 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.623 Fit side-chains REVERT: A 440 ASN cc_start: 0.8347 (p0) cc_final: 0.7934 (t0) REVERT: A 466 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7998 (ptp90) REVERT: H 117 LYS cc_start: 0.8106 (tttt) cc_final: 0.7618 (tttp) REVERT: H 148 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: H 209 LYS cc_start: 0.7140 (tptp) cc_final: 0.6851 (mmtt) REVERT: L 29 ILE cc_start: 0.8568 (mm) cc_final: 0.8340 (mm) REVERT: L 31 ASP cc_start: 0.8340 (p0) cc_final: 0.8075 (p0) REVERT: L 55 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: L 124 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7355 (tp40) REVERT: L 167 ASP cc_start: 0.7950 (t0) cc_final: 0.7285 (m-30) REVERT: L 183 LYS cc_start: 0.8360 (tptm) cc_final: 0.7706 (tptp) REVERT: L 199 GLN cc_start: 0.8597 (tt0) cc_final: 0.8233 (mt0) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.3296 time to fit residues: 34.9531 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 : 0.645 ------------------------------------------------------------------------------- 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 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 124 GLN Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 54 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3734 r_free = 0.3734 target = 0.148388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106968 restraints weight = 6325.484| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.39 r_work: 0.3071 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5051 Z= 0.240 Angle : 0.651 7.080 6878 Z= 0.321 Chirality : 0.046 0.136 769 Planarity : 0.004 0.031 885 Dihedral : 6.025 53.560 751 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 3.12 % Allowed : 14.50 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.35), residues: 629 helix: -1.26 (0.80), residues: 40 sheet: 1.04 (0.33), residues: 255 loop : -0.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE H 59 TYR 0.025 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 ********************** 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 93 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.556 Fit side-chains REVERT: A 440 ASN cc_start: 0.8317 (p0) cc_final: 0.7931 (t0) REVERT: A 466 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8053 (ptp90) REVERT: A 487 ASN cc_start: 0.7931 (m-40) cc_final: 0.7661 (m-40) REVERT: H 117 LYS cc_start: 0.8115 (tttt) cc_final: 0.7630 (tttp) REVERT: H 148 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: H 209 LYS cc_start: 0.7163 (tptp) cc_final: 0.6879 (mmtt) REVERT: L 29 ILE cc_start: 0.8575 (mm) cc_final: 0.8349 (mm) REVERT: L 31 ASP cc_start: 0.8348 (p0) cc_final: 0.8085 (p0) REVERT: L 55 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: L 167 ASP cc_start: 0.7968 (t0) cc_final: 0.7318 (m-30) REVERT: L 183 LYS cc_start: 0.8415 (tptm) cc_final: 0.7787 (tptp) REVERT: L 199 GLN cc_start: 0.8599 (tt0) cc_final: 0.8242 (mt0) outliers start: 17 outliers final: 14 residues processed: 88 average time/residue: 0.2228 time to fit residues: 24.0086 Evaluate side-chains 91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS 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 178 LEU 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 124 GLN Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 26 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3735 r_free = 0.3735 target = 0.148439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106918 restraints weight = 6292.589| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.42 r_work: 0.3088 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5051 Z= 0.239 Angle : 0.648 6.978 6878 Z= 0.320 Chirality : 0.045 0.132 769 Planarity : 0.004 0.032 885 Dihedral : 5.994 54.102 751 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 3.30 % Allowed : 14.68 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 629 helix: -1.30 (0.78), residues: 40 sheet: 1.00 (0.33), residues: 255 loop : -0.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE L 71 TYR 0.025 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.70 seconds wall clock time: 82 minutes 8.13 seconds (4928.13 seconds total)