Starting phenix.real_space_refine on Sat May 10 17:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.map" model { file = "/net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rle_19340/05_2025/8rle_19340.cif" } resolution = 3.75 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= 0.002 sd= 0.025 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2144 2.51 5 N 605 2.21 5 O 664 1.98 5 H 3190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3262 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1659 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1697 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.95, per 1000 atoms: 0.60 Number of scatterers: 6618 At special positions: 0 Unit cell: (60.58, 86.676, 82.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 664 8.00 N 605 7.00 C 2144 6.00 H 3190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 555.2 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 810 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 9.1% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.338A pdb=" N THR B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.532A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.915A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.544A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 22 removed outlier: 5.619A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 161 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 119 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 15 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 121 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 123 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.871A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 72 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.929A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.587A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.612A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN C 50 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 34 " --> pdb=" O ASN C 50 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 390 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: 2.06 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3188 1.03 - 1.23: 4 1.23 - 1.42: 1534 1.42 - 1.62: 1945 1.62 - 1.81: 22 Bond restraints: 6693 Sorted by residual: bond pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.06e+01 bond pdb=" N LEU B 207 " pdb=" CA LEU B 207 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.87e+00 bond pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.63e+00 bond pdb=" N SER B 208 " pdb=" CA SER B 208 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N GLN B 204 " pdb=" H GLN B 204 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.84e+00 ... (remaining 6688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 11249 1.07 - 2.14: 671 2.14 - 3.21: 44 3.21 - 4.28: 17 4.28 - 5.35: 1 Bond angle restraints: 11982 Sorted by residual: angle pdb=" CA SER B 208 " pdb=" C SER B 208 " pdb=" O SER B 208 " ideal model delta sigma weight residual 121.44 117.66 3.78 1.17e+00 7.31e-01 1.04e+01 angle pdb=" CA GLN B 204 " pdb=" C GLN B 204 " pdb=" O GLN B 204 " ideal model delta sigma weight residual 120.40 117.10 3.30 1.05e+00 9.07e-01 9.89e+00 angle pdb=" N PHE B 165 " pdb=" CA PHE B 165 " pdb=" C PHE B 165 " ideal model delta sigma weight residual 107.88 112.13 -4.25 1.41e+00 5.03e-01 9.08e+00 angle pdb=" CA VAL B 206 " pdb=" C VAL B 206 " pdb=" O VAL B 206 " ideal model delta sigma weight residual 120.67 117.36 3.31 1.12e+00 7.97e-01 8.76e+00 angle pdb=" CA LEU B 207 " pdb=" C LEU B 207 " pdb=" O LEU B 207 " ideal model delta sigma weight residual 120.36 117.23 3.13 1.08e+00 8.57e-01 8.42e+00 ... (remaining 11977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 2842 16.07 - 32.14: 265 32.14 - 48.22: 63 48.22 - 64.29: 32 64.29 - 80.36: 2 Dihedral angle restraints: 3204 sinusoidal: 1684 harmonic: 1520 Sorted by residual: dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS C 11 " pdb=" CB CYS C 11 " ideal model delta sinusoidal sigma weight residual -86.00 -40.18 -45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA VAL B 219 " pdb=" C VAL B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual 180.00 -164.43 -15.57 0 5.00e+00 4.00e-02 9.70e+00 dihedral pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " pdb=" OD1 ASP B 76 " ideal model delta sinusoidal sigma weight residual -30.00 -81.85 51.85 1 2.00e+01 2.50e-03 9.17e+00 ... (remaining 3201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 345 0.035 - 0.071: 111 0.071 - 0.106: 31 0.106 - 0.142: 23 0.142 - 0.177: 2 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA ILE B 152 " pdb=" N ILE B 152 " pdb=" C ILE B 152 " pdb=" CB ILE B 152 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA VAL B 206 " pdb=" N VAL B 206 " pdb=" C VAL B 206 " pdb=" CB VAL B 206 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA LEU B 207 " pdb=" N LEU B 207 " pdb=" C LEU B 207 " pdb=" CB LEU B 207 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 509 not shown) Planarity restraints: 1059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 204 " 0.224 2.00e-02 2.50e+03 3.99e-01 2.39e+03 pdb=" CD GLN B 204 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN B 204 " -0.213 2.00e-02 2.50e+03 pdb=" NE2 GLN B 204 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 204 " -0.650 2.00e-02 2.50e+03 pdb="HE22 GLN B 204 " 0.662 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 165 " -0.010 2.00e-02 2.50e+03 6.68e-03 1.34e+00 pdb=" CG PHE B 165 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 165 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 165 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 165 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 165 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 165 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 165 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 165 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 165 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 165 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 165 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 67 " 0.005 2.00e-02 2.50e+03 6.17e-03 1.14e+00 pdb=" CG PHE C 67 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE C 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 67 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 67 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE C 67 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 67 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE C 67 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE C 67 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE C 67 " -0.001 2.00e-02 2.50e+03 ... (remaining 1056 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 685 2.23 - 2.82: 14170 2.82 - 3.42: 16695 3.42 - 4.01: 22815 4.01 - 4.60: 33307 Nonbonded interactions: 87672 Sorted by model distance: nonbonded pdb="HH12 ARG C 38 " pdb=" OD1 ASP C 89 " model vdw 1.640 2.450 nonbonded pdb=" OH TYR D 59 " pdb=" H ILE D 69 " model vdw 1.681 2.450 nonbonded pdb=" OE1 GLU B 142 " pdb=" H GLU B 142 " model vdw 1.749 2.450 nonbonded pdb=" HH TYR D 59 " pdb=" H ILE D 69 " model vdw 1.749 2.100 nonbonded pdb=" O VAL B 171 " pdb=" H GLY B 174 " model vdw 1.800 2.450 ... (remaining 87667 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.120 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 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 0.038 3506 Z= 0.163 Angle : 0.557 5.355 4759 Z= 0.314 Chirality : 0.045 0.177 512 Planarity : 0.004 0.034 630 Dihedral : 13.168 80.362 1240 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.41 (0.39), residues: 444 helix: -0.82 (1.03), residues: 29 sheet: 0.67 (0.39), residues: 191 loop : 0.19 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 47 HIS 0.005 0.001 HIS B 217 PHE 0.020 0.001 PHE B 165 TYR 0.008 0.001 TYR B 143 ARG 0.004 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.10365 ( 150) hydrogen bonds : angle 6.62804 ( 390) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.38479 ( 6) covalent geometry : bond 0.00270 ( 3503) covalent geometry : angle 0.55725 ( 4753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8079 (mt) cc_final: 0.7788 (mt) REVERT: B 182 TYR cc_start: 0.7036 (t80) cc_final: 0.6566 (t80) REVERT: C 113 THR cc_start: 0.8566 (t) cc_final: 0.7878 (t) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3262 time to fit residues: 47.7795 Evaluate side-chains 112 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.162609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.140352 restraints weight = 20831.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.146628 restraints weight = 9062.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.150361 restraints weight = 4747.116| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3506 Z= 0.120 Angle : 0.526 4.564 4759 Z= 0.281 Chirality : 0.043 0.141 512 Planarity : 0.004 0.025 630 Dihedral : 4.006 12.850 493 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.41 % Allowed : 11.58 % Favored : 87.01 % 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: 0.41 (0.39), residues: 444 helix: -0.93 (0.96), residues: 28 sheet: 0.65 (0.37), residues: 205 loop : 0.20 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.012 0.001 PHE C 67 TYR 0.007 0.001 TYR C 108 ARG 0.003 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 150) hydrogen bonds : angle 6.05900 ( 390) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.52968 ( 6) covalent geometry : bond 0.00252 ( 3503) covalent geometry : angle 0.52572 ( 4753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8228 (mt) cc_final: 0.7966 (mt) REVERT: B 182 TYR cc_start: 0.6994 (t80) cc_final: 0.6542 (t80) REVERT: C 99 LEU cc_start: 0.7903 (mp) cc_final: 0.7673 (mp) REVERT: C 113 THR cc_start: 0.8200 (t) cc_final: 0.7929 (t) outliers start: 5 outliers final: 3 residues processed: 115 average time/residue: 0.3241 time to fit residues: 44.8901 Evaluate side-chains 116 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain C residue 98 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 135 ASN B 144 ASN B 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.151705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129996 restraints weight = 20386.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.135860 restraints weight = 8795.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.139422 restraints weight = 4647.691| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3506 Z= 0.254 Angle : 0.661 5.332 4759 Z= 0.365 Chirality : 0.045 0.133 512 Planarity : 0.006 0.082 630 Dihedral : 5.123 16.993 493 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.69 % Allowed : 15.82 % Favored : 82.49 % 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: -0.15 (0.40), residues: 444 helix: -1.45 (0.88), residues: 28 sheet: 0.24 (0.36), residues: 217 loop : -0.11 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 36 HIS 0.007 0.002 HIS B 217 PHE 0.024 0.003 PHE C 67 TYR 0.020 0.002 TYR D 91 ARG 0.005 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 150) hydrogen bonds : angle 6.63936 ( 390) SS BOND : bond 0.00223 ( 3) SS BOND : angle 1.09832 ( 6) covalent geometry : bond 0.00542 ( 3503) covalent geometry : angle 0.66005 ( 4753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8234 (mt) cc_final: 0.7962 (mt) REVERT: B 182 TYR cc_start: 0.6946 (t80) cc_final: 0.6513 (t80) REVERT: D 19 ARG cc_start: 0.7387 (ttp-170) cc_final: 0.6962 (ttp-170) REVERT: C 113 THR cc_start: 0.8457 (t) cc_final: 0.8213 (t) outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.3601 time to fit residues: 53.5981 Evaluate side-chains 122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.154584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132814 restraints weight = 20630.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.138782 restraints weight = 8818.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142428 restraints weight = 4638.835| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3506 Z= 0.127 Angle : 0.539 4.972 4759 Z= 0.287 Chirality : 0.044 0.136 512 Planarity : 0.004 0.031 630 Dihedral : 4.455 15.840 493 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 18.08 % Favored : 80.23 % 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: -0.05 (0.40), residues: 444 helix: -1.81 (0.90), residues: 25 sheet: 0.52 (0.38), residues: 193 loop : -0.21 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 101 HIS 0.006 0.001 HIS B 181 PHE 0.011 0.001 PHE C 67 TYR 0.009 0.001 TYR D 91 ARG 0.004 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 150) hydrogen bonds : angle 6.26310 ( 390) SS BOND : bond 0.00189 ( 3) SS BOND : angle 1.18388 ( 6) covalent geometry : bond 0.00270 ( 3503) covalent geometry : angle 0.53739 ( 4753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8202 (mt) cc_final: 0.7935 (mt) REVERT: B 182 TYR cc_start: 0.6958 (t80) cc_final: 0.6545 (t80) REVERT: D 106 GLN cc_start: 0.8066 (pp30) cc_final: 0.7701 (pp30) REVERT: C 113 THR cc_start: 0.8360 (t) cc_final: 0.8158 (t) outliers start: 6 outliers final: 5 residues processed: 116 average time/residue: 0.3423 time to fit residues: 47.4954 Evaluate side-chains 119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128592 restraints weight = 20281.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134480 restraints weight = 8638.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.138089 restraints weight = 4525.284| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3506 Z= 0.201 Angle : 0.595 5.237 4759 Z= 0.324 Chirality : 0.044 0.151 512 Planarity : 0.006 0.072 630 Dihedral : 4.813 17.396 493 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.39 % Allowed : 18.64 % Favored : 77.97 % 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 (0.40), residues: 444 helix: -1.42 (0.96), residues: 28 sheet: 0.09 (0.37), residues: 203 loop : -0.30 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 109 HIS 0.005 0.002 HIS B 217 PHE 0.015 0.002 PHE C 102 TYR 0.014 0.002 TYR D 91 ARG 0.006 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 150) hydrogen bonds : angle 6.47349 ( 390) SS BOND : bond 0.00114 ( 3) SS BOND : angle 1.49115 ( 6) covalent geometry : bond 0.00429 ( 3503) covalent geometry : angle 0.59303 ( 4753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 44 LEU cc_start: 0.8289 (mt) cc_final: 0.7997 (mt) REVERT: B 182 TYR cc_start: 0.6938 (t80) cc_final: 0.6542 (t80) REVERT: D 31 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7649 (mtt90) REVERT: D 106 GLN cc_start: 0.8156 (pp30) cc_final: 0.7706 (pp30) REVERT: C 109 TRP cc_start: 0.8854 (m100) cc_final: 0.8577 (m100) REVERT: C 113 THR cc_start: 0.8451 (t) cc_final: 0.8241 (t) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.3799 time to fit residues: 57.6882 Evaluate side-chains 130 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.130871 restraints weight = 20737.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136716 restraints weight = 9094.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140338 restraints weight = 4897.514| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3506 Z= 0.139 Angle : 0.548 5.327 4759 Z= 0.294 Chirality : 0.044 0.129 512 Planarity : 0.005 0.045 630 Dihedral : 4.510 15.766 493 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.54 % Allowed : 21.47 % Favored : 75.99 % 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: -0.30 (0.40), residues: 444 helix: -2.06 (0.90), residues: 25 sheet: 0.21 (0.36), residues: 213 loop : -0.26 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.004 0.001 HIS B 181 PHE 0.010 0.001 PHE C 67 TYR 0.008 0.001 TYR D 91 ARG 0.004 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 150) hydrogen bonds : angle 6.28325 ( 390) SS BOND : bond 0.00113 ( 3) SS BOND : angle 1.28845 ( 6) covalent geometry : bond 0.00295 ( 3503) covalent geometry : angle 0.54650 ( 4753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8235 (mt) cc_final: 0.8000 (mt) REVERT: B 81 HIS cc_start: 0.6958 (m90) cc_final: 0.6540 (m90) REVERT: B 182 TYR cc_start: 0.6855 (t80) cc_final: 0.6507 (t80) REVERT: D 5 VAL cc_start: 0.8570 (t) cc_final: 0.8114 (p) REVERT: D 106 GLN cc_start: 0.8099 (pp30) cc_final: 0.7601 (pp30) REVERT: C 113 THR cc_start: 0.8391 (t) cc_final: 0.8163 (t) outliers start: 9 outliers final: 6 residues processed: 122 average time/residue: 0.3181 time to fit residues: 47.0162 Evaluate side-chains 122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.151520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.130054 restraints weight = 20749.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135764 restraints weight = 9194.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.139287 restraints weight = 4983.722| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3506 Z= 0.152 Angle : 0.567 5.552 4759 Z= 0.304 Chirality : 0.044 0.132 512 Planarity : 0.004 0.034 630 Dihedral : 4.513 15.535 493 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.54 % Allowed : 21.75 % Favored : 75.71 % 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 (0.40), residues: 444 helix: -2.09 (0.90), residues: 25 sheet: 0.17 (0.36), residues: 213 loop : -0.32 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 101 HIS 0.004 0.001 HIS B 217 PHE 0.011 0.001 PHE C 67 TYR 0.010 0.001 TYR D 91 ARG 0.005 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 150) hydrogen bonds : angle 6.29828 ( 390) SS BOND : bond 0.00167 ( 3) SS BOND : angle 1.44933 ( 6) covalent geometry : bond 0.00323 ( 3503) covalent geometry : angle 0.56512 ( 4753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8256 (mt) cc_final: 0.7972 (mt) REVERT: B 182 TYR cc_start: 0.6838 (t80) cc_final: 0.6502 (t80) REVERT: D 106 GLN cc_start: 0.8146 (pp30) cc_final: 0.7637 (pp30) REVERT: C 113 THR cc_start: 0.8410 (t) cc_final: 0.8189 (t) outliers start: 9 outliers final: 5 residues processed: 123 average time/residue: 0.3307 time to fit residues: 48.8502 Evaluate side-chains 126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127649 restraints weight = 20756.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133436 restraints weight = 9134.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137014 restraints weight = 4929.398| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3506 Z= 0.165 Angle : 0.575 5.883 4759 Z= 0.309 Chirality : 0.044 0.130 512 Planarity : 0.004 0.037 630 Dihedral : 4.581 15.627 493 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.69 % Allowed : 21.75 % Favored : 76.55 % 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: -0.63 (0.40), residues: 444 helix: -2.16 (0.90), residues: 25 sheet: 0.01 (0.37), residues: 202 loop : -0.50 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.011 0.002 PHE C 67 TYR 0.013 0.001 TYR D 32 ARG 0.005 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 150) hydrogen bonds : angle 6.32854 ( 390) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.40690 ( 6) covalent geometry : bond 0.00348 ( 3503) covalent geometry : angle 0.57269 ( 4753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.9262 (m110) cc_final: 0.9042 (m-40) REVERT: B 182 TYR cc_start: 0.6850 (t80) cc_final: 0.6519 (t80) REVERT: D 35 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7316 (mtt180) REVERT: D 106 GLN cc_start: 0.8164 (pp30) cc_final: 0.7641 (pp30) REVERT: C 113 THR cc_start: 0.8406 (t) cc_final: 0.8180 (t) outliers start: 6 outliers final: 6 residues processed: 125 average time/residue: 0.3296 time to fit residues: 49.4198 Evaluate side-chains 125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128630 restraints weight = 20707.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134401 restraints weight = 9108.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137995 restraints weight = 4901.543| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3506 Z= 0.139 Angle : 0.578 5.963 4759 Z= 0.307 Chirality : 0.044 0.138 512 Planarity : 0.004 0.037 630 Dihedral : 4.477 15.043 493 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.98 % Allowed : 23.16 % Favored : 74.86 % 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: -0.60 (0.40), residues: 444 helix: -2.05 (0.91), residues: 25 sheet: -0.01 (0.37), residues: 202 loop : -0.46 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.003 0.001 HIS B 217 PHE 0.017 0.001 PHE B 71 TYR 0.010 0.001 TYR D 32 ARG 0.004 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 150) hydrogen bonds : angle 6.32323 ( 390) SS BOND : bond 0.00158 ( 3) SS BOND : angle 1.44666 ( 6) covalent geometry : bond 0.00296 ( 3503) covalent geometry : angle 0.57593 ( 4753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 HIS cc_start: 0.6969 (m90) cc_final: 0.6535 (m90) REVERT: B 182 TYR cc_start: 0.6849 (t80) cc_final: 0.6524 (t80) REVERT: D 106 GLN cc_start: 0.8158 (pp30) cc_final: 0.7632 (pp30) REVERT: C 113 THR cc_start: 0.8376 (t) cc_final: 0.8139 (t) outliers start: 7 outliers final: 6 residues processed: 122 average time/residue: 0.3228 time to fit residues: 47.2846 Evaluate side-chains 125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 217 HIS ** 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 = 0.4099 r_free = 0.4099 target = 0.150626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.128713 restraints weight = 20657.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134486 restraints weight = 8998.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138088 restraints weight = 4830.802| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3506 Z= 0.136 Angle : 0.573 5.962 4759 Z= 0.307 Chirality : 0.044 0.147 512 Planarity : 0.005 0.059 630 Dihedral : 4.407 14.432 493 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.54 % Allowed : 22.03 % Favored : 75.42 % 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: -0.51 (0.41), residues: 444 helix: -2.01 (0.91), residues: 25 sheet: 0.09 (0.36), residues: 213 loop : -0.45 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.004 0.001 HIS B 217 PHE 0.015 0.002 PHE B 71 TYR 0.007 0.001 TYR D 91 ARG 0.004 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 150) hydrogen bonds : angle 6.23569 ( 390) SS BOND : bond 0.00166 ( 3) SS BOND : angle 1.44187 ( 6) covalent geometry : bond 0.00289 ( 3503) covalent geometry : angle 0.57117 ( 4753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 HIS cc_start: 0.6946 (m90) cc_final: 0.6509 (m90) REVERT: B 182 TYR cc_start: 0.6845 (t80) cc_final: 0.6526 (t80) REVERT: D 71 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6679 (ttp-170) REVERT: D 106 GLN cc_start: 0.8124 (pp30) cc_final: 0.7575 (pp30) REVERT: C 113 THR cc_start: 0.8343 (t) cc_final: 0.8096 (t) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.3171 time to fit residues: 48.2686 Evaluate side-chains 126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 HIS ** 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 = 0.4082 r_free = 0.4082 target = 0.149355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127089 restraints weight = 20536.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132931 restraints weight = 8952.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136539 restraints weight = 4812.035| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3506 Z= 0.160 Angle : 0.590 6.004 4759 Z= 0.319 Chirality : 0.045 0.153 512 Planarity : 0.005 0.054 630 Dihedral : 4.534 13.791 493 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.26 % Allowed : 22.32 % Favored : 75.42 % 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: -0.65 (0.41), residues: 444 helix: -2.09 (0.92), residues: 25 sheet: 0.04 (0.37), residues: 213 loop : -0.61 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.005 0.001 HIS B 217 PHE 0.019 0.002 PHE B 71 TYR 0.013 0.001 TYR D 32 ARG 0.006 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 150) hydrogen bonds : angle 6.31133 ( 390) SS BOND : bond 0.00159 ( 3) SS BOND : angle 1.50179 ( 6) covalent geometry : bond 0.00340 ( 3503) covalent geometry : angle 0.58832 ( 4753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.44 seconds wall clock time: 60 minutes 21.18 seconds (3621.18 seconds total)