Starting phenix.real_space_refine on Tue Feb 3 16:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1p_62751/02_2026/9l1p_62751.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3255 2.51 5 N 877 2.21 5 O 1018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5173 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "E" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 1.42, per 1000 atoms: 0.27 Number of scatterers: 5173 At special positions: 0 Unit cell: (118.483, 77.177, 63.046, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1018 8.00 N 877 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.00 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=1.96 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.14 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.10 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=2.14 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.01 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=1.97 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: 0.46 Conformation dependent library (CDL) restraints added in 415.4 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 5.1% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.529A pdb=" N ARG E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.671A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.623A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 186 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.752A pdb=" N ALA B 109 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.101A pdb=" N ILE B 39 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA B 143 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 41 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'E' and resid 40 through 42 removed outlier: 6.183A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 removed outlier: 5.704A pdb=" N ALA H 16 " --> pdb=" O ARG H 85 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG H 85 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.189A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.189A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.743A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 186 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 161 through 163 removed outlier: 4.378A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.862A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 150 174 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 1138 1.32 - 1.47: 1796 1.47 - 1.63: 2317 1.63 - 1.78: 13 1.78 - 1.94: 24 Bond restraints: 5288 Sorted by residual: bond pdb=" CD2 HIS E 53 " pdb=" NE2 HIS E 53 " ideal model delta sigma weight residual 1.374 1.465 -0.091 1.10e-02 8.26e+03 6.88e+01 bond pdb=" CA ASP H 110 " pdb=" C ASP H 110 " ideal model delta sigma weight residual 1.519 1.602 -0.083 1.01e-02 9.80e+03 6.71e+01 bond pdb=" ND1 HIS L 198 " pdb=" CE1 HIS L 198 " ideal model delta sigma weight residual 1.321 1.402 -0.081 1.00e-02 1.00e+04 6.64e+01 bond pdb=" CA LEU L 175 " pdb=" C LEU L 175 " ideal model delta sigma weight residual 1.523 1.611 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA TYR L 186 " pdb=" C TYR L 186 " ideal model delta sigma weight residual 1.519 1.612 -0.093 1.19e-02 7.06e+03 6.15e+01 ... (remaining 5283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 5163 2.58 - 5.17: 1555 5.17 - 7.75: 396 7.75 - 10.33: 56 10.33 - 12.92: 5 Bond angle restraints: 7175 Sorted by residual: angle pdb=" ND1 HIS H 209 " pdb=" CE1 HIS H 209 " pdb=" NE2 HIS H 209 " ideal model delta sigma weight residual 108.40 116.83 -8.43 1.00e+00 1.00e+00 7.10e+01 angle pdb=" OE1 GLN L 124 " pdb=" CD GLN L 124 " pdb=" NE2 GLN L 124 " ideal model delta sigma weight residual 122.60 114.58 8.02 1.00e+00 1.00e+00 6.43e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 108.36 119.54 -11.18 1.43e+00 4.89e-01 6.11e+01 angle pdb=" N VAL H 191 " pdb=" CA VAL H 191 " pdb=" C VAL H 191 " ideal model delta sigma weight residual 108.48 119.46 -10.98 1.44e+00 4.82e-01 5.81e+01 angle pdb=" N TYR L 186 " pdb=" CA TYR L 186 " pdb=" C TYR L 186 " ideal model delta sigma weight residual 113.43 104.11 9.32 1.26e+00 6.30e-01 5.47e+01 ... (remaining 7170 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.23: 2949 17.23 - 34.45: 186 34.45 - 51.68: 32 51.68 - 68.90: 7 68.90 - 86.13: 9 Dihedral angle restraints: 3183 sinusoidal: 1245 harmonic: 1938 Sorted by residual: dihedral pdb=" CA ARG B 65 " pdb=" C ARG B 65 " pdb=" N TRP B 66 " pdb=" CA TRP B 66 " ideal model delta harmonic sigma weight residual 180.00 145.31 34.69 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 205 " pdb=" CB CYS H 205 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 0.00 -30.86 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 3180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 473 0.160 - 0.319: 240 0.319 - 0.479: 60 0.479 - 0.639: 20 0.639 - 0.799: 5 Chirality restraints: 798 Sorted by residual: chirality pdb=" CG LEU B 138 " pdb=" CB LEU B 138 " pdb=" CD1 LEU B 138 " pdb=" CD2 LEU B 138 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CB THR B 116 " pdb=" CA THR B 116 " pdb=" OG1 THR B 116 " pdb=" CG2 THR B 116 " both_signs ideal model delta sigma weight residual False 2.55 1.81 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CB THR L 172 " pdb=" CA THR L 172 " pdb=" OG1 THR L 172 " pdb=" CG2 THR L 172 " both_signs ideal model delta sigma weight residual False 2.55 1.82 0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 795 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 116 " -0.034 2.00e-02 2.50e+03 7.79e-02 1.06e+02 pdb=" CG PHE L 116 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 PHE L 116 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE L 116 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 PHE L 116 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE L 116 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE L 116 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 203 " -0.073 2.00e-02 2.50e+03 6.81e-02 9.26e+01 pdb=" CG TYR H 203 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR H 203 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR H 203 " 0.100 2.00e-02 2.50e+03 pdb=" CE1 TYR H 203 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR H 203 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR H 203 " -0.056 2.00e-02 2.50e+03 pdb=" OH TYR H 203 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 64 " 0.031 2.00e-02 2.50e+03 6.60e-02 7.63e+01 pdb=" CG PHE H 64 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE H 64 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 PHE H 64 " -0.101 2.00e-02 2.50e+03 pdb=" CE1 PHE H 64 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE H 64 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 64 " 0.083 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 928 2.77 - 3.30: 4752 3.30 - 3.83: 7775 3.83 - 4.37: 9726 4.37 - 4.90: 17339 Nonbonded interactions: 40520 Sorted by model distance: nonbonded pdb=" NE2 HIS H 173 " pdb=" OD1 ASN L 137 " model vdw 2.236 3.120 nonbonded pdb=" O TYR L 186 " pdb=" O HIS L 189 " model vdw 2.419 3.040 nonbonded pdb=" N PHE B 98 " pdb=" O PHE B 98 " model vdw 2.430 2.496 nonbonded pdb=" N ASN H 55 " pdb=" O ASN H 55 " model vdw 2.443 2.496 nonbonded pdb=" O ASN H 52 " pdb=" O ASN H 55 " model vdw 2.455 3.040 ... (remaining 40515 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.035 0.163 5295 Z= 2.172 Angle : 2.613 16.632 7189 Z= 1.699 Chirality : 0.206 0.799 798 Planarity : 0.023 0.097 924 Dihedral : 12.940 86.126 1922 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.30), residues: 662 helix: -5.38 (0.17), residues: 12 sheet: -1.50 (0.30), residues: 280 loop : -2.31 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.007 ARG B 50 TYR 0.120 0.026 TYR E 79 PHE 0.109 0.031 PHE B 98 TRP 0.100 0.029 TRP B 66 HIS 0.083 0.016 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.03458 ( 5288) covalent geometry : angle 2.58510 ( 7175) SS BOND : bond 0.07483 ( 7) SS BOND : angle 9.03116 ( 14) hydrogen bonds : bond 0.17485 ( 169) hydrogen bonds : angle 8.98182 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.203 Fit side-chains REVERT: B 46 ASN cc_start: 0.7065 (m-40) cc_final: 0.6732 (m110) REVERT: L 149 LYS cc_start: 0.5980 (mttt) cc_final: 0.5545 (mtpp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0645 time to fit residues: 7.8798 Evaluate side-chains 81 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN L 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.184953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.171948 restraints weight = 5980.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.172752 restraints weight = 3893.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.173209 restraints weight = 3154.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.174222 restraints weight = 2589.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.174241 restraints weight = 2241.677| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5295 Z= 0.195 Angle : 0.721 7.337 7189 Z= 0.378 Chirality : 0.048 0.171 798 Planarity : 0.006 0.056 924 Dihedral : 5.971 23.815 725 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.26 % Allowed : 5.03 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.31), residues: 662 helix: -5.31 (0.17), residues: 12 sheet: -1.20 (0.30), residues: 289 loop : -1.99 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 85 TYR 0.014 0.002 TYR E 127 PHE 0.017 0.003 PHE L 139 TRP 0.014 0.002 TRP H 112 HIS 0.009 0.002 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5288) covalent geometry : angle 0.71930 ( 7175) SS BOND : bond 0.00383 ( 7) SS BOND : angle 1.37420 ( 14) hydrogen bonds : bond 0.04043 ( 169) hydrogen bonds : angle 7.33990 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.197 Fit side-chains REVERT: E 142 LYS cc_start: 0.8013 (mttm) cc_final: 0.7647 (mttm) REVERT: H 109 MET cc_start: 0.9042 (mpp) cc_final: 0.8650 (mtm) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.0553 time to fit residues: 7.1244 Evaluate side-chains 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 185 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.0060 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 164 ASN L 6 GLN L 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.188005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.174958 restraints weight = 5951.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.175735 restraints weight = 4278.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.176223 restraints weight = 3194.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.177547 restraints weight = 2690.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.177645 restraints weight = 2222.497| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5295 Z= 0.127 Angle : 0.616 7.364 7189 Z= 0.321 Chirality : 0.045 0.152 798 Planarity : 0.005 0.053 924 Dihedral : 5.295 21.321 725 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.26 % Allowed : 9.03 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.32), residues: 662 helix: -5.25 (0.19), residues: 12 sheet: -1.00 (0.30), residues: 284 loop : -1.77 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.016 0.001 TYR E 134 PHE 0.012 0.002 PHE L 139 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5288) covalent geometry : angle 0.61509 ( 7175) SS BOND : bond 0.00363 ( 7) SS BOND : angle 0.94580 ( 14) hydrogen bonds : bond 0.03129 ( 169) hydrogen bonds : angle 6.75960 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7294 (tt0) cc_final: 0.7081 (tt0) REVERT: B 89 MET cc_start: 0.7867 (mtt) cc_final: 0.7643 (mtt) REVERT: H 70 LEU cc_start: 0.8115 (mp) cc_final: 0.7867 (mt) REVERT: H 109 MET cc_start: 0.8982 (mpp) cc_final: 0.8554 (mtm) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.0677 time to fit residues: 7.6206 Evaluate side-chains 87 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.184260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.173643 restraints weight = 6018.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.173308 restraints weight = 6357.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.173282 restraints weight = 3904.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.173741 restraints weight = 3026.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.173920 restraints weight = 2537.527| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5295 Z= 0.187 Angle : 0.659 7.228 7189 Z= 0.344 Chirality : 0.047 0.168 798 Planarity : 0.005 0.056 924 Dihedral : 5.449 20.867 725 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.30 % Allowed : 9.20 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.32), residues: 662 helix: -5.24 (0.19), residues: 12 sheet: -1.06 (0.29), residues: 298 loop : -1.83 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 101 TYR 0.013 0.002 TYR L 87 PHE 0.015 0.002 PHE L 73 TRP 0.009 0.002 TRP B 66 HIS 0.006 0.002 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5288) covalent geometry : angle 0.65736 ( 7175) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.17665 ( 14) hydrogen bonds : bond 0.03498 ( 169) hydrogen bonds : angle 6.90416 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.166 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 89 average time/residue: 0.0516 time to fit residues: 6.0520 Evaluate side-chains 93 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 185 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.185947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.172747 restraints weight = 6054.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173754 restraints weight = 4549.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.174171 restraints weight = 3449.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.174831 restraints weight = 2878.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.175028 restraints weight = 2355.953| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5295 Z= 0.157 Angle : 0.619 7.156 7189 Z= 0.323 Chirality : 0.046 0.153 798 Planarity : 0.005 0.060 924 Dihedral : 5.273 20.693 725 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.65 % Allowed : 9.90 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.32), residues: 662 helix: -5.22 (0.20), residues: 12 sheet: -1.06 (0.30), residues: 290 loop : -1.73 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 211 TYR 0.011 0.002 TYR B 126 PHE 0.013 0.002 PHE L 139 TRP 0.010 0.002 TRP B 66 HIS 0.006 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5288) covalent geometry : angle 0.61733 ( 7175) SS BOND : bond 0.00278 ( 7) SS BOND : angle 1.10227 ( 14) hydrogen bonds : bond 0.03252 ( 169) hydrogen bonds : angle 6.76169 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.117 Fit side-chains REVERT: L 36 TYR cc_start: 0.8799 (m-80) cc_final: 0.8509 (m-80) REVERT: L 89 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (pt0) outliers start: 21 outliers final: 14 residues processed: 86 average time/residue: 0.0505 time to fit residues: 5.6966 Evaluate side-chains 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.187621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.174329 restraints weight = 6068.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.175483 restraints weight = 4471.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.175715 restraints weight = 3292.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.176205 restraints weight = 3065.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.176722 restraints weight = 2522.114| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5295 Z= 0.124 Angle : 0.574 7.114 7189 Z= 0.300 Chirality : 0.044 0.150 798 Planarity : 0.005 0.061 924 Dihedral : 4.944 20.395 725 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.17 % Allowed : 10.42 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.32), residues: 662 helix: -5.22 (0.20), residues: 12 sheet: -0.96 (0.30), residues: 290 loop : -1.57 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 TYR 0.009 0.001 TYR B 126 PHE 0.012 0.002 PHE B 67 TRP 0.011 0.001 TRP B 66 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5288) covalent geometry : angle 0.57309 ( 7175) SS BOND : bond 0.00226 ( 7) SS BOND : angle 0.86700 ( 14) hydrogen bonds : bond 0.02937 ( 169) hydrogen bonds : angle 6.47013 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: L 36 TYR cc_start: 0.8762 (m-80) cc_final: 0.8555 (m-80) REVERT: L 135 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6227 (tt) REVERT: L 149 LYS cc_start: 0.5834 (mttt) cc_final: 0.5498 (mttm) outliers start: 24 outliers final: 18 residues processed: 90 average time/residue: 0.0561 time to fit residues: 6.5721 Evaluate side-chains 97 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 39 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.187809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3843 r_free = 0.3843 target = 0.174749 restraints weight = 5925.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.175357 restraints weight = 6042.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.176372 restraints weight = 3871.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.176734 restraints weight = 3244.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.177056 restraints weight = 2537.715| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5295 Z= 0.125 Angle : 0.578 6.990 7189 Z= 0.300 Chirality : 0.044 0.151 798 Planarity : 0.005 0.064 924 Dihedral : 4.859 19.967 725 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.82 % Allowed : 10.94 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.32), residues: 662 helix: -5.20 (0.21), residues: 12 sheet: -0.90 (0.30), residues: 290 loop : -1.50 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.009 0.001 TYR B 126 PHE 0.012 0.002 PHE L 73 TRP 0.010 0.001 TRP B 66 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5288) covalent geometry : angle 0.57693 ( 7175) SS BOND : bond 0.00226 ( 7) SS BOND : angle 0.85573 ( 14) hydrogen bonds : bond 0.02960 ( 169) hydrogen bonds : angle 6.39037 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: L 135 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6260 (tt) REVERT: L 149 LYS cc_start: 0.5823 (mttt) cc_final: 0.5505 (mttm) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 0.0524 time to fit residues: 6.0702 Evaluate side-chains 96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 11 optimal weight: 0.0040 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.188411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.176371 restraints weight = 5942.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.176420 restraints weight = 6294.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.176851 restraints weight = 3903.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.177265 restraints weight = 2977.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.178086 restraints weight = 2438.262| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5295 Z= 0.125 Angle : 0.571 6.919 7189 Z= 0.298 Chirality : 0.044 0.153 798 Planarity : 0.005 0.064 924 Dihedral : 4.793 19.886 725 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.47 % Allowed : 11.28 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.32), residues: 662 helix: -5.19 (0.21), residues: 12 sheet: -0.79 (0.30), residues: 284 loop : -1.50 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.010 0.001 TYR E 134 PHE 0.012 0.002 PHE L 73 TRP 0.010 0.001 TRP B 66 HIS 0.006 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5288) covalent geometry : angle 0.57046 ( 7175) SS BOND : bond 0.00234 ( 7) SS BOND : angle 0.82214 ( 14) hydrogen bonds : bond 0.02925 ( 169) hydrogen bonds : angle 6.33788 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: L 135 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6208 (tt) REVERT: L 149 LYS cc_start: 0.5850 (mttt) cc_final: 0.5493 (mttm) outliers start: 20 outliers final: 18 residues processed: 86 average time/residue: 0.0808 time to fit residues: 9.0356 Evaluate side-chains 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.185446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.174828 restraints weight = 5972.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.174757 restraints weight = 5605.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.175403 restraints weight = 4682.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.175454 restraints weight = 3775.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.175522 restraints weight = 3525.888| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5295 Z= 0.175 Angle : 0.621 6.987 7189 Z= 0.324 Chirality : 0.046 0.154 798 Planarity : 0.005 0.065 924 Dihedral : 5.116 20.187 725 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.12 % Allowed : 11.98 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.32), residues: 662 helix: -5.20 (0.20), residues: 12 sheet: -0.95 (0.29), residues: 298 loop : -1.59 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.012 0.002 TYR L 87 PHE 0.015 0.002 PHE B 127 TRP 0.008 0.002 TRP B 66 HIS 0.007 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5288) covalent geometry : angle 0.62046 ( 7175) SS BOND : bond 0.00267 ( 7) SS BOND : angle 0.91318 ( 14) hydrogen bonds : bond 0.03351 ( 169) hydrogen bonds : angle 6.59509 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: E 63 MET cc_start: 0.7775 (mtm) cc_final: 0.7502 (mpp) REVERT: L 135 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6462 (tt) REVERT: L 149 LYS cc_start: 0.5781 (mttt) cc_final: 0.5459 (mttm) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.0838 time to fit residues: 9.6446 Evaluate side-chains 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.184710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.173812 restraints weight = 6004.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.173450 restraints weight = 6349.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.174111 restraints weight = 5203.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.174529 restraints weight = 3936.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.174543 restraints weight = 3472.087| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5295 Z= 0.180 Angle : 0.628 6.934 7189 Z= 0.329 Chirality : 0.046 0.157 798 Planarity : 0.005 0.066 924 Dihedral : 5.211 20.443 725 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.65 % Allowed : 11.81 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.32), residues: 662 helix: -5.20 (0.19), residues: 12 sheet: -1.04 (0.29), residues: 298 loop : -1.66 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.012 0.002 TYR B 126 PHE 0.014 0.002 PHE L 73 TRP 0.009 0.002 TRP B 66 HIS 0.007 0.002 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 5288) covalent geometry : angle 0.62683 ( 7175) SS BOND : bond 0.00340 ( 7) SS BOND : angle 0.94283 ( 14) hydrogen bonds : bond 0.03357 ( 169) hydrogen bonds : angle 6.69579 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: L 135 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6438 (tt) REVERT: L 149 LYS cc_start: 0.5773 (mttt) cc_final: 0.5441 (mttm) outliers start: 21 outliers final: 18 residues processed: 92 average time/residue: 0.0643 time to fit residues: 7.8639 Evaluate side-chains 102 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 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 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.184989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.171984 restraints weight = 6162.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.170181 restraints weight = 6586.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.171738 restraints weight = 4273.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.172988 restraints weight = 3097.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.173494 restraints weight = 2460.706| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5295 Z= 0.163 Angle : 0.609 6.885 7189 Z= 0.318 Chirality : 0.045 0.153 798 Planarity : 0.005 0.067 924 Dihedral : 5.122 20.511 725 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.65 % Allowed : 11.98 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.32), residues: 662 helix: -5.20 (0.19), residues: 12 sheet: -1.03 (0.29), residues: 298 loop : -1.65 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.011 0.002 TYR L 87 PHE 0.014 0.002 PHE L 73 TRP 0.009 0.002 TRP B 66 HIS 0.006 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5288) covalent geometry : angle 0.60869 ( 7175) SS BOND : bond 0.00335 ( 7) SS BOND : angle 0.91285 ( 14) hydrogen bonds : bond 0.03266 ( 169) hydrogen bonds : angle 6.64582 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 954.28 seconds wall clock time: 17 minutes 15.84 seconds (1035.84 seconds total)