Starting phenix.real_space_refine on Thu Oct 22 20:12:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.cif Found real_map, /net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.map" model { file = "/net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22pl_68584/10_2026/22pl_68584.cif" } resolution = 3.3 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= 0.007 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 24 5.16 5 C 3061 2.51 5 N 803 2.21 5 O 948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4836 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1007 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 118} Chain: "B" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1688 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 194} Chain: "C" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2046 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 244} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.26, per 1000 atoms: 0.26 Number of scatterers: 4836 At special positions: 0 Unit cell: (85.118, 94.754, 111.617, 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 24 16.00 O 948 8.00 N 803 7.00 C 3061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 215 " distance=2.03 Simple disulfide: pdb=" SG CYS C 245 " - pdb=" SG CYS C 255 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 301 " - " ASN B 67 " " NAG C 401 " - " ASN C 163 " " NAG D 1 " - " ASN B 93 " " NAG E 1 " - " ASN B 37 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 173.5 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 10 sheets defined 15.0% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 34 through 58 removed outlier: 3.655A pdb=" N ILE A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.977A pdb=" N LYS A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 157 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.930A pdb=" N ALA B 79 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 42 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASN B 37 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 32 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 39 " --> pdb=" O CYS B 30 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 30 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR B 41 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 28 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LYS B 121 " --> pdb=" O CYS B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 32 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 70 removed outlier: 3.714A pdb=" N GLU B 101 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 70 removed outlier: 3.714A pdb=" N GLU B 101 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.512A pdb=" N ARG B 129 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 188 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 177 removed outlier: 3.993A pdb=" N MET B 171 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 162 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.639A pdb=" N LYS C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 82 removed outlier: 7.649A pdb=" N ILE C 71 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL C 82 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE C 69 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN C 68 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 115 " --> pdb=" O GLN C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 152 Processing sheet with id=AA9, first strand: chain 'C' and resid 157 through 159 removed outlier: 6.684A pdb=" N VAL C 158 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.580A pdb=" N LYS C 286 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 277 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 306 " --> pdb=" O PHE C 325 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 480 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: 0.69 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1534 1.34 - 1.46: 958 1.46 - 1.58: 2417 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 4941 Sorted by residual: bond pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.07e+00 bond pdb=" CA GLN C 300 " pdb=" C GLN C 300 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.34e-02 5.57e+03 3.59e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C ILE C 298 " pdb=" O ILE C 298 " ideal model delta sigma weight residual 1.236 1.220 0.017 1.19e-02 7.06e+03 1.92e+00 ... (remaining 4936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6494 1.63 - 3.27: 161 3.27 - 4.90: 29 4.90 - 6.54: 12 6.54 - 8.17: 4 Bond angle restraints: 6700 Sorted by residual: angle pdb=" N SER B 167 " pdb=" CA SER B 167 " pdb=" C SER B 167 " ideal model delta sigma weight residual 110.53 116.62 -6.09 1.32e+00 5.74e-01 2.13e+01 angle pdb=" N GLN C 300 " pdb=" CA GLN C 300 " pdb=" C GLN C 300 " ideal model delta sigma weight residual 110.80 118.00 -7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" N GLN C 297 " pdb=" CA GLN C 297 " pdb=" C GLN C 297 " ideal model delta sigma weight residual 113.29 119.94 -6.65 2.00e+00 2.50e-01 1.10e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" C THR B 164 " ideal model delta sigma weight residual 109.46 104.13 5.33 1.66e+00 3.63e-01 1.03e+01 angle pdb=" N GLN C 303 " pdb=" CA GLN C 303 " pdb=" C GLN C 303 " ideal model delta sigma weight residual 108.69 114.28 -5.59 1.77e+00 3.19e-01 9.98e+00 ... (remaining 6695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 2719 21.58 - 43.15: 317 43.15 - 64.73: 40 64.73 - 86.31: 12 86.31 - 107.88: 5 Dihedral angle restraints: 3093 sinusoidal: 1365 harmonic: 1728 Sorted by residual: dihedral pdb=" CB CYS B 68 " pdb=" SG CYS B 68 " pdb=" SG CYS B 81 " pdb=" CB CYS B 81 " ideal model delta sinusoidal sigma weight residual 93.00 177.04 -84.04 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS C 245 " pdb=" SG CYS C 245 " pdb=" SG CYS C 255 " pdb=" CB CYS C 255 " ideal model delta sinusoidal sigma weight residual 93.00 27.84 65.16 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" C GLN C 297 " pdb=" N GLN C 297 " pdb=" CA GLN C 297 " pdb=" CB GLN C 297 " ideal model delta harmonic sigma weight residual -122.60 -134.63 12.03 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 3090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 728 0.100 - 0.200: 38 0.200 - 0.300: 4 0.300 - 0.400: 0 0.400 - 0.500: 1 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA GLN C 297 " pdb=" N GLN C 297 " pdb=" C GLN C 297 " pdb=" CB GLN C 297 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA VAL B 165 " pdb=" N VAL B 165 " pdb=" C VAL B 165 " pdb=" CB VAL B 165 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 768 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C THR B 164 " 0.058 2.00e-02 2.50e+03 pdb=" O THR B 164 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL B 165 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 79 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO A 80 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 295 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ASN C 295 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN C 295 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP C 296 " -0.011 2.00e-02 2.50e+03 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 344 2.74 - 3.28: 4680 3.28 - 3.82: 7847 3.82 - 4.36: 8942 4.36 - 4.90: 15831 Nonbonded interactions: 37644 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" OG SER C 98 " model vdw 2.196 3.040 nonbonded pdb=" O LEU A 152 " pdb=" OG1 THR A 156 " model vdw 2.278 3.040 nonbonded pdb=" O THR C 299 " pdb=" OH TYR C 306 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR C 252 " pdb=" N GLN C 297 " model vdw 2.317 3.120 nonbonded pdb=" OG1 THR A 130 " pdb=" OD2 ASP C 155 " model vdw 2.319 3.040 ... (remaining 37639 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: 2.130 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4955 Z= 0.166 Angle : 0.666 8.169 6735 Z= 0.348 Chirality : 0.051 0.500 771 Planarity : 0.005 0.079 841 Dihedral : 17.711 107.883 1942 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.37 % Allowed : 28.81 % Favored : 70.83 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 15.38 % 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: -0.48 (0.35), residues: 573 helix: 2.17 (0.55), residues: 78 sheet: -0.32 (0.42), residues: 161 loop : -0.93 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.022 0.002 TYR B 34 PHE 0.013 0.001 PHE B 194 TRP 0.010 0.001 TRP C 81 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 ( 4941) covalent geometry : angle 0.66283 / 0.35 ( 6700) SS BOND : bond 0.00255 / 0.13 ( 7) SS BOND : angle 0.80210 / 0.45 ( 14) hydrogen bonds : bond 0.23790 / 15.55 ( 157) hydrogen bonds : angle 9.32870 / 6.50 ( 480) link_BETA1-4 : bond 0.00687 / 0.34 ( 3) link_BETA1-4 : angle 1.41416 / 0.66 ( 9) link_NAG-ASN : bond 0.00155 / 0.08 ( 4) link_NAG-ASN : angle 1.23835 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.134 Fit side-chains REVERT: C 113 ARG cc_start: 0.6022 (ptt180) cc_final: 0.5821 (ptt90) outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.0817 time to fit residues: 7.2848 Evaluate side-chains 63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 297 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 50] chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN B 77 ASN C 51 GLN C 110 HIS C 175 ASN C 176 ASN C 190 GLN C 270 GLN C 290 HIS C 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.196717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165360 restraints weight = 5982.029| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.46 r_work: 0.3743 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4955 Z= 0.154 Angle : 0.610 9.184 6735 Z= 0.309 Chirality : 0.044 0.184 771 Planarity : 0.005 0.060 841 Dihedral : 9.887 75.524 768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 3.12 % Allowed : 24.95 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.44 (0.34), residues: 573 helix: 1.90 (0.53), residues: 79 sheet: -0.18 (0.39), residues: 183 loop : -0.92 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 319 TYR 0.024 0.002 TYR C 168 PHE 0.019 0.001 PHE C 325 TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4941) covalent geometry : angle 0.60393 / 0.31 ( 6700) SS BOND : bond 0.00376 / 0.20 ( 7) SS BOND : angle 1.01360 / 0.57 ( 14) hydrogen bonds : bond 0.05407 / 3.58 ( 157) hydrogen bonds : angle 6.22815 / 4.24 ( 480) link_BETA1-4 : bond 0.00958 / 0.48 ( 3) link_BETA1-4 : angle 1.90123 / 0.94 ( 9) link_NAG-ASN : bond 0.00188 / 0.09 ( 4) link_NAG-ASN : angle 1.09076 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.182 Fit side-chains REVERT: B 199 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7870 (mt) REVERT: C 226 MET cc_start: 0.8348 (tmm) cc_final: 0.7996 (tmm) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.0604 time to fit residues: 6.5183 Evaluate side-chains 74 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [25, 48, 17, 44, 0, 13, 53, 45, 29, 19, 27] chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.193916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.159048 restraints weight = 5924.099| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.36 r_work: 0.3728 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4955 Z= 0.169 Angle : 0.602 9.938 6735 Z= 0.299 Chirality : 0.044 0.186 771 Planarity : 0.004 0.044 841 Dihedral : 7.722 50.776 765 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.03 % Rotamer: Outliers : 4.77 % Allowed : 23.30 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.43 (0.34), residues: 573 helix: 1.84 (0.54), residues: 79 sheet: -0.14 (0.38), residues: 189 loop : -0.94 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.021 0.002 TYR C 168 PHE 0.011 0.001 PHE C 325 TRP 0.008 0.001 TRP B 211 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 4941) covalent geometry : angle 0.59634 / 0.30 ( 6700) SS BOND : bond 0.00480 / 0.25 ( 7) SS BOND : angle 1.11078 / 0.63 ( 14) hydrogen bonds : bond 0.04876 / 3.22 ( 157) hydrogen bonds : angle 5.53239 / 3.78 ( 480) link_BETA1-4 : bond 0.00847 / 0.43 ( 3) link_BETA1-4 : angle 1.72948 / 0.84 ( 9) link_NAG-ASN : bond 0.00243 / 0.12 ( 4) link_NAG-ASN : angle 1.15051 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8014 (ptpt) REVERT: B 36 LYS cc_start: 0.7927 (mptt) cc_final: 0.7482 (mptt) REVERT: B 199 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8004 (mt) REVERT: C 226 MET cc_start: 0.8392 (tmm) cc_final: 0.8011 (tmm) outliers start: 26 outliers final: 13 residues processed: 89 average time/residue: 0.0667 time to fit residues: 7.6904 Evaluate side-chains 77 residues out of total 545 (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 42 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [17, 55, 20, 1, 32, 49, 38, 0, 36, 24, 15] chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.193442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158938 restraints weight = 5860.606| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.34 r_work: 0.3730 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4955 Z= 0.152 Angle : 0.581 10.527 6735 Z= 0.286 Chirality : 0.043 0.180 771 Planarity : 0.004 0.041 841 Dihedral : 6.610 49.677 765 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 4.04 % Allowed : 24.04 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.46 (0.34), residues: 573 helix: 1.65 (0.56), residues: 81 sheet: -0.07 (0.38), residues: 187 loop : -0.99 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.022 0.002 TYR C 168 PHE 0.017 0.001 PHE C 325 TRP 0.007 0.001 TRP B 211 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 4941) covalent geometry : angle 0.57475 / 0.28 ( 6700) SS BOND : bond 0.00454 / 0.24 ( 7) SS BOND : angle 1.19976 / 0.68 ( 14) hydrogen bonds : bond 0.04479 / 2.96 ( 157) hydrogen bonds : angle 5.26705 / 3.59 ( 480) link_BETA1-4 : bond 0.00794 / 0.40 ( 3) link_BETA1-4 : angle 1.68635 / 0.78 ( 9) link_NAG-ASN : bond 0.00212 / 0.11 ( 4) link_NAG-ASN : angle 1.16731 / 0.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8058 (ptpt) REVERT: B 36 LYS cc_start: 0.7909 (mptt) cc_final: 0.7458 (mptt) REVERT: B 138 ARG cc_start: 0.7485 (ptp-110) cc_final: 0.7188 (ptp-110) REVERT: B 199 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8009 (mt) outliers start: 22 outliers final: 13 residues processed: 80 average time/residue: 0.0744 time to fit residues: 7.6817 Evaluate side-chains 70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [0, 5, 31, 17, 42, 56, 36, 18, 27, 38, 43] chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155274 restraints weight = 5985.466| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.53 r_work: 0.3695 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4955 Z= 0.175 Angle : 0.588 10.907 6735 Z= 0.290 Chirality : 0.043 0.190 771 Planarity : 0.004 0.040 841 Dihedral : 5.718 49.931 765 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.86 % Rotamer: Outliers : 4.40 % Allowed : 23.12 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.53 (0.34), residues: 573 helix: 1.59 (0.56), residues: 81 sheet: -0.15 (0.37), residues: 187 loop : -1.01 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.021 0.002 TYR C 168 PHE 0.011 0.001 PHE C 325 TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 4941) covalent geometry : angle 0.58177 / 0.29 ( 6700) SS BOND : bond 0.00501 / 0.27 ( 7) SS BOND : angle 1.15379 / 0.65 ( 14) hydrogen bonds : bond 0.04499 / 2.99 ( 157) hydrogen bonds : angle 5.20854 / 3.56 ( 480) link_BETA1-4 : bond 0.00722 / 0.36 ( 3) link_BETA1-4 : angle 1.62047 / 0.73 ( 9) link_NAG-ASN : bond 0.00224 / 0.11 ( 4) link_NAG-ASN : angle 1.25126 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7874 (ptpt) REVERT: B 36 LYS cc_start: 0.8029 (mptt) cc_final: 0.7458 (mptt) REVERT: B 199 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8060 (mt) outliers start: 24 outliers final: 17 residues processed: 80 average time/residue: 0.0782 time to fit residues: 7.9206 Evaluate side-chains 76 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [8, 4, 36, 55, 13, 5, 2, 3, 6, 14, 29] chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.195238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162869 restraints weight = 5973.195| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.62 r_work: 0.3725 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4955 Z= 0.116 Angle : 0.552 11.775 6735 Z= 0.271 Chirality : 0.042 0.177 771 Planarity : 0.004 0.041 841 Dihedral : 5.423 50.134 765 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 3.49 % Allowed : 24.95 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.38 (0.34), residues: 573 helix: 1.93 (0.56), residues: 79 sheet: -0.06 (0.37), residues: 187 loop : -0.95 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.022 0.002 TYR B 34 PHE 0.019 0.001 PHE C 325 TRP 0.007 0.001 TRP C 257 HIS 0.005 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4941) covalent geometry : angle 0.54692 / 0.27 ( 6700) SS BOND : bond 0.00334 / 0.18 ( 7) SS BOND : angle 1.05175 / 0.60 ( 14) hydrogen bonds : bond 0.04161 / 2.76 ( 157) hydrogen bonds : angle 4.97050 / 3.40 ( 480) link_BETA1-4 : bond 0.00733 / 0.37 ( 3) link_BETA1-4 : angle 1.47241 / 0.68 ( 9) link_NAG-ASN : bond 0.00172 / 0.09 ( 4) link_NAG-ASN : angle 1.09165 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LYS cc_start: 0.7773 (mptt) cc_final: 0.7308 (mptt) REVERT: B 94 TYR cc_start: 0.8592 (m-10) cc_final: 0.8366 (m-10) REVERT: B 111 MET cc_start: 0.8431 (mmt) cc_final: 0.7817 (mmt) REVERT: B 199 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7976 (mt) REVERT: C 226 MET cc_start: 0.8346 (tmm) cc_final: 0.8072 (tmm) REVERT: C 300 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.5026 (tm-30) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.0700 time to fit residues: 7.6513 Evaluate side-chains 77 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [44, 50, 23, 56, 7, 26, 37, 32, 34, 2, 49] chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.0170 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.195221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162901 restraints weight = 5954.669| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.67 r_work: 0.3734 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4955 Z= 0.119 Angle : 0.576 12.483 6735 Z= 0.279 Chirality : 0.042 0.182 771 Planarity : 0.004 0.041 841 Dihedral : 5.286 50.755 765 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 3.67 % Allowed : 24.22 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.31 (0.35), residues: 573 helix: 1.86 (0.57), residues: 81 sheet: 0.00 (0.38), residues: 190 loop : -0.90 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 202 TYR 0.022 0.002 TYR B 34 PHE 0.011 0.001 PHE C 325 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4941) covalent geometry : angle 0.56439 / 0.27 ( 6700) SS BOND : bond 0.00355 / 0.19 ( 7) SS BOND : angle 2.17437 / 1.38 ( 14) hydrogen bonds : bond 0.04123 / 2.72 ( 157) hydrogen bonds : angle 4.85895 / 3.32 ( 480) link_BETA1-4 : bond 0.00690 / 0.35 ( 3) link_BETA1-4 : angle 1.41277 / 0.65 ( 9) link_NAG-ASN : bond 0.00165 / 0.08 ( 4) link_NAG-ASN : angle 1.08793 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LYS cc_start: 0.7705 (mptt) cc_final: 0.7265 (mptt) REVERT: B 94 TYR cc_start: 0.8601 (m-10) cc_final: 0.8347 (m-10) REVERT: B 199 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 51 GLN cc_start: 0.6387 (mm110) cc_final: 0.6178 (mm-40) REVERT: C 300 GLN cc_start: 0.5486 (OUTLIER) cc_final: 0.5061 (tm-30) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.0743 time to fit residues: 7.4796 Evaluate side-chains 78 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [26, 37, 4, 50, 43, 38, 39, 47, 41, 17, 3] chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.0050 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.194027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162413 restraints weight = 5961.927| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.53 r_work: 0.3730 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4955 Z= 0.130 Angle : 0.570 12.766 6735 Z= 0.276 Chirality : 0.042 0.184 771 Planarity : 0.004 0.042 841 Dihedral : 5.200 50.466 765 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 3.67 % Allowed : 25.14 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.28 (0.34), residues: 573 helix: 1.84 (0.57), residues: 81 sheet: 0.13 (0.38), residues: 188 loop : -0.96 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 202 TYR 0.024 0.002 TYR B 34 PHE 0.019 0.001 PHE C 325 TRP 0.010 0.001 TRP C 267 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 4941) covalent geometry : angle 0.56183 / 0.27 ( 6700) SS BOND : bond 0.00431 / 0.23 ( 7) SS BOND : angle 1.75208 / 1.10 ( 14) hydrogen bonds : bond 0.04141 / 2.73 ( 157) hydrogen bonds : angle 4.79000 / 3.27 ( 480) link_BETA1-4 : bond 0.00701 / 0.35 ( 3) link_BETA1-4 : angle 1.40910 / 0.65 ( 9) link_NAG-ASN : bond 0.00166 / 0.08 ( 4) link_NAG-ASN : angle 1.10949 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LYS cc_start: 0.7750 (mptt) cc_final: 0.7309 (mptt) REVERT: B 94 TYR cc_start: 0.8593 (m-10) cc_final: 0.8330 (m-10) REVERT: B 199 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 300 GLN cc_start: 0.5507 (OUTLIER) cc_final: 0.5115 (tm-30) outliers start: 20 outliers final: 15 residues processed: 79 average time/residue: 0.0745 time to fit residues: 7.5186 Evaluate side-chains 78 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [23, 38, 37, 45, 21, 26, 15, 4, 16, 55, 42] chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.195873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159563 restraints weight = 5889.121| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.49 r_work: 0.3744 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4955 Z= 0.118 Angle : 0.564 13.080 6735 Z= 0.272 Chirality : 0.042 0.183 771 Planarity : 0.004 0.042 841 Dihedral : 5.119 50.258 765 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 3.12 % Allowed : 25.32 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 (0.35), residues: 573 helix: 1.87 (0.57), residues: 81 sheet: 0.15 (0.39), residues: 190 loop : -0.89 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 319 TYR 0.024 0.002 TYR B 34 PHE 0.009 0.001 PHE C 325 TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 4941) covalent geometry : angle 0.55694 / 0.27 ( 6700) SS BOND : bond 0.00314 / 0.17 ( 7) SS BOND : angle 1.56954 / 0.98 ( 14) hydrogen bonds : bond 0.04045 / 2.67 ( 157) hydrogen bonds : angle 4.71551 / 3.22 ( 480) link_BETA1-4 : bond 0.00698 / 0.35 ( 3) link_BETA1-4 : angle 1.36249 / 0.63 ( 9) link_NAG-ASN : bond 0.00150 / 0.07 ( 4) link_NAG-ASN : angle 1.07990 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LYS cc_start: 0.7826 (mptt) cc_final: 0.7294 (mptt) REVERT: B 111 MET cc_start: 0.8451 (mmt) cc_final: 0.7943 (mmt) REVERT: B 199 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 300 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.5131 (tm-30) outliers start: 17 outliers final: 14 residues processed: 80 average time/residue: 0.0835 time to fit residues: 8.4434 Evaluate side-chains 78 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [45, 49, 51, 12, 55, 36, 7, 46, 17, 44, 48] chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.0030 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163180 restraints weight = 5935.649| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.32 r_work: 0.3784 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4955 Z= 0.102 Angle : 0.561 13.734 6735 Z= 0.269 Chirality : 0.041 0.178 771 Planarity : 0.004 0.042 841 Dihedral : 5.006 50.610 765 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 2.94 % Allowed : 25.69 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.07 (0.35), residues: 573 helix: 2.08 (0.55), residues: 79 sheet: 0.26 (0.39), residues: 190 loop : -0.82 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 319 TYR 0.023 0.001 TYR B 34 PHE 0.018 0.001 PHE C 325 TRP 0.007 0.001 TRP B 170 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4941) covalent geometry : angle 0.55504 / 0.27 ( 6700) SS BOND : bond 0.00265 / 0.14 ( 7) SS BOND : angle 1.44669 / 0.90 ( 14) hydrogen bonds : bond 0.03948 / 2.60 ( 157) hydrogen bonds : angle 4.62786 / 3.18 ( 480) link_BETA1-4 : bond 0.00705 / 0.36 ( 3) link_BETA1-4 : angle 1.34573 / 0.63 ( 9) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 0.99677 / 0.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (mt) REVERT: C 300 GLN cc_start: 0.5540 (OUTLIER) cc_final: 0.5134 (tm-30) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.0649 time to fit residues: 6.2181 Evaluate side-chains 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: [2, 13, 8, 47, 33, 37, 40, 46, 19, 14, 39] chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159375 restraints weight = 5928.556| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.38 r_work: 0.3737 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4955 Z= 0.153 Angle : 0.588 13.156 6735 Z= 0.283 Chirality : 0.042 0.192 771 Planarity : 0.004 0.049 841 Dihedral : 5.113 50.600 765 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.03 % Rotamer: Outliers : 2.75 % Allowed : 25.87 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.18 (0.35), residues: 573 helix: 1.99 (0.56), residues: 79 sheet: 0.18 (0.38), residues: 194 loop : -0.89 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 319 TYR 0.026 0.002 TYR B 34 PHE 0.009 0.001 PHE C 152 TRP 0.009 0.001 TRP B 214 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4941) covalent geometry : angle 0.58131 / 0.28 ( 6700) SS BOND : bond 0.00421 / 0.22 ( 7) SS BOND : angle 1.46129 / 0.90 ( 14) hydrogen bonds : bond 0.04200 / 2.77 ( 157) hydrogen bonds : angle 4.75074 / 3.25 ( 480) link_BETA1-4 : bond 0.00684 / 0.35 ( 3) link_BETA1-4 : angle 1.42206 / 0.66 ( 9) link_NAG-ASN : bond 0.00167 / 0.08 ( 4) link_NAG-ASN : angle 1.18461 / 0.63 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.04 seconds wall clock time: 26 minutes 8.77 seconds (1568.77 seconds total)