Starting phenix.real_space_refine on Sun Apr 27 23:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rle_19340/04_2025/8rle_19340.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rle_19340/04_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_19340/04_2025/8rle_19340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rle_19340/04_2025/8rle_19340.map" model { file = "/net/cci-nas-00/data/ceres_data/8rle_19340/04_2025/8rle_19340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rle_19340/04_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-5669/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: 3.82, per 1000 atoms: 0.58 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: 1.69 Conformation dependent library (CDL) restraints added in 650.4 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: 0.54 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: 2.03 Time building geometry restraints manager: 2.08 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: 2.300 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.250 Find NCS groups from input model: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- 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 : 0.528 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: 0.3762 time to fit residues: 54.8408 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 : 1.240 ------------------------------------------------------------------------------- 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 = 0.162608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.140357 restraints weight = 20831.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.146614 restraints weight = 9059.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150353 restraints weight = 4753.544| |-----------------------------------------------------------------------------| 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 4.563 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 0.00354 ( 3) SS BOND : angle 0.52967 ( 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 : 1.305 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: 0.6541 (t80) REVERT: C 99 LEU cc_start: 0.7903 (mp) cc_final: 0.7673 (mp) REVERT: C 113 THR cc_start: 0.8199 (t) cc_final: 0.7929 (t) outliers start: 5 outliers final: 3 residues processed: 115 average time/residue: 0.5912 time to fit residues: 85.2020 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 : 1.587 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 144 ASN B 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132376 restraints weight = 20418.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.138249 restraints weight = 8804.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141891 restraints weight = 4639.772| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3506 Z= 0.213 Angle : 0.605 4.849 4759 Z= 0.332 Chirality : 0.044 0.131 512 Planarity : 0.005 0.061 630 Dihedral : 4.697 15.466 493 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.41 % Allowed : 15.82 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.40), residues: 444 helix: -1.14 (0.92), residues: 28 sheet: 0.38 (0.36), residues: 220 loop : 0.11 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 101 HIS 0.006 0.001 HIS B 217 PHE 0.021 0.002 PHE C 67 TYR 0.017 0.002 TYR D 91 ARG 0.005 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 150) hydrogen bonds : angle 6.34690 ( 390) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.06008 ( 6) covalent geometry : bond 0.00448 ( 3503) covalent geometry : angle 0.60459 ( 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 128 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.487 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 44 LEU cc_start: 0.8216 (mt) cc_final: 0.7937 (mt) REVERT: B 96 ARG cc_start: 0.6505 (mtp180) cc_final: 0.6238 (mtp180) REVERT: B 170 ASN cc_start: 0.9215 (m110) cc_final: 0.8970 (m110) REVERT: B 182 TYR cc_start: 0.6938 (t80) cc_final: 0.6511 (t80) REVERT: B 204 GLN cc_start: 0.7905 (tt0) cc_final: 0.7638 (tt0) REVERT: D 35 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7434 (mtt180) REVERT: C 71 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7532 (ttm110) REVERT: C 113 THR cc_start: 0.8420 (t) cc_final: 0.8162 (t) outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.4539 time to fit residues: 66.8746 Evaluate side-chains 119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 77 THR 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: 0.6980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN B 177 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.132887 restraints weight = 20707.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.138870 restraints weight = 8852.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142535 restraints weight = 4635.860| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3506 Z= 0.146 Angle : 0.543 5.047 4759 Z= 0.291 Chirality : 0.044 0.132 512 Planarity : 0.004 0.033 630 Dihedral : 4.404 15.757 493 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.69 % Allowed : 18.36 % Favored : 79.94 % 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: -1.70 (0.94), residues: 25 sheet: 0.54 (0.38), residues: 199 loop : -0.12 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.013 0.001 PHE C 67 TYR 0.012 0.001 TYR D 91 ARG 0.004 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 150) hydrogen bonds : angle 6.21211 ( 390) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.11297 ( 6) covalent geometry : bond 0.00313 ( 3503) covalent geometry : angle 0.54176 ( 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 118 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8198 (mt) cc_final: 0.7926 (mt) REVERT: B 182 TYR cc_start: 0.6957 (t80) cc_final: 0.6527 (t80) REVERT: B 204 GLN cc_start: 0.7874 (tt0) cc_final: 0.7572 (tt0) REVERT: D 106 GLN cc_start: 0.8088 (pp30) cc_final: 0.7764 (pp30) REVERT: C 71 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7435 (ttm110) outliers start: 6 outliers final: 2 residues processed: 114 average time/residue: 0.3471 time to fit residues: 47.4976 Evaluate side-chains 113 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain D residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.153388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131638 restraints weight = 20579.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137643 restraints weight = 8852.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141256 restraints weight = 4608.405| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.3783 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= 0.146 Angle : 0.540 4.876 4759 Z= 0.289 Chirality : 0.043 0.143 512 Planarity : 0.004 0.041 630 Dihedral : 4.376 15.606 493 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.54 % Allowed : 18.93 % Favored : 78.53 % 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: 0.01 (0.40), residues: 444 helix: -1.74 (0.94), residues: 25 sheet: 0.56 (0.37), residues: 204 loop : -0.21 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.012 0.001 PHE C 67 TYR 0.010 0.001 TYR D 91 ARG 0.004 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 150) hydrogen bonds : angle 6.11621 ( 390) SS BOND : bond 0.00177 ( 3) SS BOND : angle 1.22472 ( 6) covalent geometry : bond 0.00310 ( 3503) covalent geometry : angle 0.53850 ( 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 128 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.536 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 44 LEU cc_start: 0.8245 (mt) cc_final: 0.7980 (mt) REVERT: B 182 TYR cc_start: 0.6938 (t80) cc_final: 0.6524 (t80) REVERT: B 204 GLN cc_start: 0.7873 (tt0) cc_final: 0.7482 (tt0) REVERT: D 106 GLN cc_start: 0.8069 (pp30) cc_final: 0.7648 (pp30) outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 0.3595 time to fit residues: 51.9770 Evaluate side-chains 121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL 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: 1.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.151647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.129926 restraints weight = 20403.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.135866 restraints weight = 8738.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.139440 restraints weight = 4580.208| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3506 Z= 0.171 Angle : 0.562 5.390 4759 Z= 0.302 Chirality : 0.043 0.129 512 Planarity : 0.005 0.049 630 Dihedral : 4.535 15.969 493 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.82 % Allowed : 20.34 % Favored : 76.84 % 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: -0.17 (0.40), residues: 444 helix: -2.12 (0.92), residues: 25 sheet: 0.48 (0.36), residues: 204 loop : -0.35 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 109 HIS 0.004 0.001 HIS B 217 PHE 0.013 0.002 PHE C 67 TYR 0.011 0.001 TYR D 91 ARG 0.005 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 150) hydrogen bonds : angle 6.20509 ( 390) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.13524 ( 6) covalent geometry : bond 0.00362 ( 3503) covalent geometry : angle 0.56074 ( 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 130 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8288 (mt) cc_final: 0.7985 (mt) REVERT: B 182 TYR cc_start: 0.6918 (t80) cc_final: 0.6531 (t80) REVERT: B 204 GLN cc_start: 0.7928 (tt0) cc_final: 0.7680 (tt0) REVERT: D 101 TRP cc_start: 0.7892 (m100) cc_final: 0.7564 (m100) REVERT: D 106 GLN cc_start: 0.8102 (pp30) cc_final: 0.7667 (pp30) REVERT: C 98 ARG cc_start: 0.6853 (ttp80) cc_final: 0.6605 (ttp80) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.3452 time to fit residues: 51.6307 Evaluate side-chains 125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 105 THR 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: 0.3980 chunk 29 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.153165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131157 restraints weight = 20315.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137053 restraints weight = 8676.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.140602 restraints weight = 4558.930| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3506 Z= 0.114 Angle : 0.532 5.490 4759 Z= 0.282 Chirality : 0.044 0.131 512 Planarity : 0.004 0.036 630 Dihedral : 4.264 14.581 493 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.98 % Allowed : 20.62 % Favored : 77.40 % 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: -0.09 (0.40), residues: 444 helix: -1.94 (0.92), residues: 25 sheet: 0.51 (0.36), residues: 203 loop : -0.29 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 57 HIS 0.006 0.001 HIS B 181 PHE 0.009 0.001 PHE C 67 TYR 0.009 0.001 TYR D 32 ARG 0.004 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 150) hydrogen bonds : angle 6.03387 ( 390) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.27119 ( 6) covalent geometry : bond 0.00243 ( 3503) covalent geometry : angle 0.53080 ( 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 124 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8196 (mt) cc_final: 0.7990 (mt) REVERT: B 81 HIS cc_start: 0.6947 (m90) cc_final: 0.6535 (m90) REVERT: B 182 TYR cc_start: 0.6920 (t80) cc_final: 0.6534 (t80) REVERT: B 204 GLN cc_start: 0.7922 (tt0) cc_final: 0.7720 (tt0) REVERT: D 5 VAL cc_start: 0.8520 (t) cc_final: 0.8146 (p) REVERT: D 106 GLN cc_start: 0.8079 (pp30) cc_final: 0.7590 (pp30) outliers start: 7 outliers final: 6 residues processed: 119 average time/residue: 0.3428 time to fit residues: 48.8677 Evaluate side-chains 121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 141 LEU 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 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: 3.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.130586 restraints weight = 20477.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136391 restraints weight = 8786.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.139952 restraints weight = 4591.985| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4608 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= 0.145 Angle : 0.557 5.743 4759 Z= 0.295 Chirality : 0.044 0.126 512 Planarity : 0.005 0.062 630 Dihedral : 4.345 14.607 493 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.26 % Allowed : 20.34 % Favored : 77.40 % 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: -0.24 (0.40), residues: 444 helix: -1.92 (0.94), residues: 25 sheet: 0.28 (0.36), residues: 215 loop : -0.29 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.010 0.001 PHE C 67 TYR 0.015 0.001 TYR D 32 ARG 0.006 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 150) hydrogen bonds : angle 6.14439 ( 390) SS BOND : bond 0.00170 ( 3) SS BOND : angle 1.46267 ( 6) covalent geometry : bond 0.00311 ( 3503) covalent geometry : angle 0.55461 ( 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 125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8249 (mt) cc_final: 0.8005 (mt) REVERT: B 81 HIS cc_start: 0.6949 (m90) cc_final: 0.6531 (m90) REVERT: B 182 TYR cc_start: 0.6896 (t80) cc_final: 0.6528 (t80) REVERT: B 204 GLN cc_start: 0.7910 (tt0) cc_final: 0.7681 (tt0) REVERT: D 19 ARG cc_start: 0.7179 (ttp-170) cc_final: 0.6553 (ttp-170) REVERT: D 106 GLN cc_start: 0.8085 (pp30) cc_final: 0.7598 (pp30) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.3419 time to fit residues: 49.3797 Evaluate side-chains 123 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 141 LEU 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 D residue 105 THR 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: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8664 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.150969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129535 restraints weight = 20372.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135441 restraints weight = 8701.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138960 restraints weight = 4531.547| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4878 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= 0.164 Angle : 0.572 5.847 4759 Z= 0.306 Chirality : 0.044 0.131 512 Planarity : 0.005 0.046 630 Dihedral : 4.518 15.038 493 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.26 % Allowed : 21.75 % 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: -0.34 (0.40), residues: 444 helix: -2.04 (0.93), residues: 25 sheet: 0.28 (0.36), residues: 215 loop : -0.44 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 101 HIS 0.004 0.001 HIS B 217 PHE 0.011 0.002 PHE C 102 TYR 0.015 0.001 TYR D 32 ARG 0.006 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 150) hydrogen bonds : angle 6.22587 ( 390) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.49421 ( 6) covalent geometry : bond 0.00349 ( 3503) covalent geometry : angle 0.57017 ( 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: 8 poor density : 118 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8253 (mt) cc_final: 0.8015 (mt) REVERT: B 182 TYR cc_start: 0.6908 (t80) cc_final: 0.6545 (t80) REVERT: B 204 GLN cc_start: 0.7882 (tt0) cc_final: 0.7595 (tt0) REVERT: D 19 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6557 (ttp-170) REVERT: D 95 ASN cc_start: 0.7978 (p0) cc_final: 0.7676 (p0) REVERT: D 106 GLN cc_start: 0.8113 (pp30) cc_final: 0.7606 (pp30) outliers start: 8 outliers final: 7 residues processed: 122 average time/residue: 0.3428 time to fit residues: 49.6671 Evaluate side-chains 122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 141 LEU 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 D residue 105 THR 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: 2.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128011 restraints weight = 20777.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133877 restraints weight = 9091.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137420 restraints weight = 4884.773| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3506 Z= 0.143 Angle : 0.572 9.212 4759 Z= 0.300 Chirality : 0.044 0.138 512 Planarity : 0.005 0.051 630 Dihedral : 4.440 15.099 493 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.98 % Allowed : 21.47 % 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: -0.46 (0.40), residues: 444 helix: -1.94 (0.94), residues: 25 sheet: 0.18 (0.37), residues: 204 loop : -0.47 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 109 HIS 0.004 0.001 HIS B 217 PHE 0.011 0.002 PHE C 67 TYR 0.017 0.001 TYR C 79 ARG 0.007 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 150) hydrogen bonds : angle 6.14869 ( 390) SS BOND : bond 0.00207 ( 3) SS BOND : angle 1.43275 ( 6) covalent geometry : bond 0.00304 ( 3503) covalent geometry : angle 0.57031 ( 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 126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.8221 (mt) cc_final: 0.7981 (mt) REVERT: B 81 HIS cc_start: 0.6989 (m90) cc_final: 0.6543 (m90) REVERT: B 182 TYR cc_start: 0.6863 (t80) cc_final: 0.6537 (t80) REVERT: D 19 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6547 (ttp-170) REVERT: D 106 GLN cc_start: 0.8083 (pp30) cc_final: 0.7566 (pp30) outliers start: 7 outliers final: 6 residues processed: 121 average time/residue: 0.3814 time to fit residues: 54.9634 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 : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU 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 D residue 105 THR 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: 2.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 204 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 = 0.4069 r_free = 0.4069 target = 0.148190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.126109 restraints weight = 20781.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131963 restraints weight = 9088.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135530 restraints weight = 4883.782| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5361 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= 0.181 Angle : 0.601 9.006 4759 Z= 0.318 Chirality : 0.044 0.134 512 Planarity : 0.005 0.048 630 Dihedral : 4.647 15.893 493 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.98 % Allowed : 22.03 % 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: -0.69 (0.40), residues: 444 helix: -2.13 (0.93), residues: 25 sheet: 0.04 (0.37), residues: 204 loop : -0.65 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 57 HIS 0.004 0.001 HIS B 217 PHE 0.013 0.002 PHE C 67 TYR 0.018 0.002 TYR D 32 ARG 0.007 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 150) hydrogen bonds : angle 6.31481 ( 390) SS BOND : bond 0.00178 ( 3) SS BOND : angle 1.52666 ( 6) covalent geometry : bond 0.00387 ( 3503) covalent geometry : angle 0.59885 ( 4753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4060.52 seconds wall clock time: 72 minutes 0.50 seconds (4320.50 seconds total)