Starting phenix.real_space_refine on Wed Sep 17 14:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddo_46778/09_2025/9ddo_46778.map" } resolution = 2.8 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 5921 2.51 5 N 1587 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9252 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "B" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1719 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "C" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "D" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1705 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "F" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 168 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Y" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 216 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.25 Number of scatterers: 9252 At special positions: 0 Unit cell: (83.83, 85.49, 117.86, 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 38 16.00 P 2 15.00 O 1704 8.00 N 1587 7.00 C 5921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.82 Conformation dependent library (CDL) restraints added in 235.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.577A pdb=" N GLN A 17 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 13 through 18' Processing helix chain 'A' and resid 20 through 63 removed outlier: 3.687A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 82 through 98 removed outlier: 3.506A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 127 removed outlier: 4.036A pdb=" N ILE A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 162 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 166 through 230 removed outlier: 4.321A pdb=" N VAL A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 4.446A pdb=" N ALA A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 20 through 63 Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 82 through 97 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 163 removed outlier: 3.536A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 166 through 232 removed outlier: 3.592A pdb=" N VAL B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Proline residue: B 172 - end of helix Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 11 through 18 removed outlier: 3.631A pdb=" N TYR C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 63 removed outlier: 3.507A pdb=" N VAL C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 103 through 127 removed outlier: 4.013A pdb=" N ILE C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 163 removed outlier: 3.739A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Proline residue: C 141 - end of helix removed outlier: 3.602A pdb=" N GLN C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 232 removed outlier: 4.292A pdb=" N VAL C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 3.856A pdb=" N ALA C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 11 through 18 Processing helix chain 'D' and resid 20 through 63 removed outlier: 3.958A pdb=" N VAL D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.598A pdb=" N GLU D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 127 removed outlier: 3.980A pdb=" N ILE D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 163 removed outlier: 3.816A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 170 through 231 Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 20 through 63 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 82 through 97 removed outlier: 3.536A pdb=" N LEU E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 127 Processing helix chain 'E' and resid 129 through 163 removed outlier: 3.922A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Proline residue: E 141 - end of helix Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 170 through 233 Proline residue: E 190 - end of helix Processing helix chain 'F' and resid 11 through 32 Processing helix chain 'Y' and resid 20 through 38 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Z' and resid 21 through 37 removed outlier: 4.064A pdb=" N ASP Z 25 " --> pdb=" O THR Z 21 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2430 1.33 - 1.45: 1487 1.45 - 1.57: 5394 1.57 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 9385 Sorted by residual: bond pdb=" N LEU A 145 " pdb=" CA LEU A 145 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.33e-02 5.65e+03 1.16e+01 bond pdb=" N VAL Y 20 " pdb=" CA VAL Y 20 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE Y 18 " pdb=" CA ILE Y 18 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.04e+01 bond pdb=" N HIS A 18 " pdb=" CA HIS A 18 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.22e-02 6.72e+03 9.14e+00 bond pdb=" N PHE E 78 " pdb=" CA PHE E 78 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.95e+00 ... (remaining 9380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10277 2.09 - 4.18: 2284 4.18 - 6.26: 117 6.26 - 8.35: 6 8.35 - 10.44: 2 Bond angle restraints: 12686 Sorted by residual: angle pdb=" CA ASP Z 25 " pdb=" CB ASP Z 25 " pdb=" CG ASP Z 25 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" CA GLN B 201 " pdb=" C GLN B 201 " pdb=" O GLN B 201 " ideal model delta sigma weight residual 120.42 116.19 4.23 1.06e+00 8.90e-01 1.59e+01 angle pdb=" CB HIS B 18 " pdb=" CG HIS B 18 " pdb=" CD2 HIS B 18 " ideal model delta sigma weight residual 131.20 126.02 5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" OE1 GLN E 125 " pdb=" CD GLN E 125 " pdb=" NE2 GLN E 125 " ideal model delta sigma weight residual 122.60 118.62 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N ALA E 19 " pdb=" CA ALA E 19 " pdb=" C ALA E 19 " ideal model delta sigma weight residual 110.35 115.75 -5.40 1.36e+00 5.41e-01 1.58e+01 ... (remaining 12681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.07: 5478 31.07 - 62.15: 125 62.15 - 93.22: 8 93.22 - 124.30: 0 124.30 - 155.37: 1 Dihedral angle restraints: 5612 sinusoidal: 2175 harmonic: 3437 Sorted by residual: dihedral pdb=" C3 PEV D 301 " pdb=" C1 PEV D 301 " pdb=" C2 PEV D 301 " pdb=" O3P PEV D 301 " ideal model delta sinusoidal sigma weight residual -67.20 88.17 -155.37 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA SER B 98 " pdb=" C SER B 98 " pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C ASN C 72 " pdb=" N ASN C 72 " pdb=" CA ASN C 72 " pdb=" CB ASN C 72 " ideal model delta harmonic sigma weight residual -122.60 -132.75 10.15 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 5609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1101 0.089 - 0.177: 341 0.177 - 0.266: 45 0.266 - 0.354: 8 0.354 - 0.443: 1 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2 PEV D 301 " pdb=" C1 PEV D 301 " pdb=" C3 PEV D 301 " pdb=" O2 PEV D 301 " both_signs ideal model delta sigma weight residual False 2.36 2.80 -0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA ASN C 72 " pdb=" N ASN C 72 " pdb=" C ASN C 72 " pdb=" CB ASN C 72 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA SER E 98 " pdb=" N SER E 98 " pdb=" C SER E 98 " pdb=" CB SER E 98 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1493 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 23 " 0.117 2.00e-02 2.50e+03 7.45e-02 9.70e+01 pdb=" CG PHE Y 23 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 23 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 23 " -0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 23 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE Y 23 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 16 " 0.104 2.00e-02 2.50e+03 5.60e-02 6.27e+01 pdb=" CG TYR A 16 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 16 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 16 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 16 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR A 16 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 16 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 16 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 PEV D 301 " -0.120 2.00e-02 2.50e+03 6.92e-02 4.78e+01 pdb=" C32 PEV D 301 " 0.034 2.00e-02 2.50e+03 pdb=" O2 PEV D 301 " 0.038 2.00e-02 2.50e+03 pdb=" O31 PEV D 301 " 0.047 2.00e-02 2.50e+03 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3695 2.93 - 3.43: 10423 3.43 - 3.92: 15562 3.92 - 4.41: 16047 4.41 - 4.90: 29033 Nonbonded interactions: 74760 Sorted by model distance: nonbonded pdb=" O ILE C 152 " pdb=" OG SER C 155 " model vdw 2.442 3.040 nonbonded pdb=" OE1 GLU A 94 " pdb=" NH1 ARG A 114 " model vdw 2.467 3.120 nonbonded pdb=" OE1 GLU A 58 " pdb=" OG SER A 84 " model vdw 2.570 3.040 nonbonded pdb=" OE1 GLU C 58 " pdb=" OG SER C 84 " model vdw 2.575 3.040 nonbonded pdb=" OE2 GLU D 58 " pdb=" OG SER D 82 " model vdw 2.576 3.040 ... (remaining 74755 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 9 through 232) selection = chain 'C' selection = (chain 'D' and resid 9 through 232) selection = (chain 'E' and resid 9 through 232) } ncs_group { reference = (chain 'Y' and resid 12 through 39) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.530 Find NCS groups from input model: 0.170 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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 : 0.011 0.050 9385 Z= 0.685 Angle : 1.614 10.438 12686 Z= 1.119 Chirality : 0.083 0.443 1496 Planarity : 0.014 0.117 1618 Dihedral : 13.503 155.372 3392 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.74 % Allowed : 5.27 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.22), residues: 1193 helix: 0.83 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 222 TYR 0.104 0.022 TYR A 16 PHE 0.117 0.010 PHE Y 23 TRP 0.088 0.015 TRP B 13 HIS 0.013 0.002 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.01108 ( 9385) covalent geometry : angle 1.61410 (12686) hydrogen bonds : bond 0.15129 ( 856) hydrogen bonds : angle 6.19296 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 381 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TRP cc_start: 0.9323 (t-100) cc_final: 0.8678 (t-100) REVERT: A 16 TYR cc_start: 0.9165 (t80) cc_final: 0.8955 (t80) REVERT: A 17 GLN cc_start: 0.9120 (mt0) cc_final: 0.8691 (mm110) REVERT: A 18 HIS cc_start: 0.7952 (p-80) cc_final: 0.7582 (p-80) REVERT: A 58 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8801 (mt-10) REVERT: A 60 GLN cc_start: 0.9163 (tt0) cc_final: 0.8833 (tm-30) REVERT: A 86 HIS cc_start: 0.8414 (t70) cc_final: 0.7642 (t70) REVERT: A 90 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 92 GLN cc_start: 0.9018 (tp40) cc_final: 0.8452 (tm-30) REVERT: A 94 GLU cc_start: 0.8978 (tp30) cc_final: 0.8469 (tp30) REVERT: A 96 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 105 GLU cc_start: 0.8767 (mp0) cc_final: 0.8544 (mp0) REVERT: A 109 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8653 (pt0) REVERT: A 223 ASP cc_start: 0.8975 (m-30) cc_final: 0.8715 (m-30) REVERT: B 47 GLU cc_start: 0.8983 (tp30) cc_final: 0.8645 (tp30) REVERT: B 52 LYS cc_start: 0.9252 (ttpp) cc_final: 0.8955 (ttpp) REVERT: B 64 GLU cc_start: 0.9016 (pm20) cc_final: 0.8723 (pm20) REVERT: B 86 HIS cc_start: 0.8819 (t70) cc_final: 0.8555 (t70) REVERT: B 90 GLU cc_start: 0.8631 (tp30) cc_final: 0.8155 (tp30) REVERT: B 94 GLU cc_start: 0.9372 (tp30) cc_final: 0.9014 (tp30) REVERT: B 116 GLU cc_start: 0.9049 (tp30) cc_final: 0.8837 (tp30) REVERT: B 166 ASN cc_start: 0.8929 (m110) cc_final: 0.8635 (m110) REVERT: B 200 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8424 (ttm170) REVERT: B 223 ASP cc_start: 0.9226 (t70) cc_final: 0.8901 (t0) REVERT: C 15 MET cc_start: 0.9067 (mtp) cc_final: 0.8818 (mtp) REVERT: C 18 HIS cc_start: 0.8417 (t70) cc_final: 0.7819 (t-90) REVERT: C 64 GLU cc_start: 0.8880 (tp30) cc_final: 0.8213 (tp30) REVERT: C 72 ASN cc_start: 0.8833 (p0) cc_final: 0.8332 (p0) REVERT: C 94 GLU cc_start: 0.8999 (tp30) cc_final: 0.8736 (mm-30) REVERT: C 96 GLU cc_start: 0.9000 (pt0) cc_final: 0.8752 (pt0) REVERT: C 103 ASP cc_start: 0.8993 (t0) cc_final: 0.8787 (t0) REVERT: C 104 ASN cc_start: 0.9211 (m-40) cc_final: 0.8976 (m-40) REVERT: C 109 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8732 (tp30) REVERT: C 116 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 117 ARG cc_start: 0.9078 (mmm160) cc_final: 0.8399 (mmm-85) REVERT: C 161 GLN cc_start: 0.9448 (mt0) cc_final: 0.8956 (mp10) REVERT: C 227 GLU cc_start: 0.9182 (tp30) cc_final: 0.8809 (tp30) REVERT: D 18 HIS cc_start: 0.9046 (t70) cc_final: 0.8665 (t-90) REVERT: D 20 ASP cc_start: 0.8617 (t70) cc_final: 0.8345 (t0) REVERT: D 50 ASN cc_start: 0.9223 (m-40) cc_final: 0.8776 (m-40) REVERT: D 69 ASN cc_start: 0.9332 (m-40) cc_final: 0.9122 (m-40) REVERT: D 89 ASN cc_start: 0.9354 (m110) cc_final: 0.9135 (m-40) REVERT: D 94 GLU cc_start: 0.9288 (tp30) cc_final: 0.8868 (mm-30) REVERT: D 103 ASP cc_start: 0.9186 (t0) cc_final: 0.8969 (t0) REVERT: D 176 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8455 (mt-10) REVERT: D 227 GLU cc_start: 0.9054 (tp30) cc_final: 0.8608 (tp30) REVERT: E 47 GLU cc_start: 0.8887 (tp30) cc_final: 0.8671 (tp30) REVERT: E 86 HIS cc_start: 0.8711 (t70) cc_final: 0.7995 (t70) REVERT: E 94 GLU cc_start: 0.8976 (tp30) cc_final: 0.8442 (tp30) REVERT: E 109 GLU cc_start: 0.8980 (tp30) cc_final: 0.8662 (tp30) REVERT: E 174 ILE cc_start: 0.9494 (pt) cc_final: 0.9268 (pt) REVERT: E 227 GLU cc_start: 0.9207 (tp30) cc_final: 0.8807 (tp30) REVERT: Z 19 ASN cc_start: 0.9261 (t0) cc_final: 0.9046 (t0) outliers start: 7 outliers final: 1 residues processed: 385 average time/residue: 0.5753 time to fit residues: 234.6121 Evaluate side-chains 299 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 59 GLN A 215 GLN B 50 ASN B 130 ASN C 60 GLN C 89 ASN C 154 ASN D 72 ASN D 89 ASN Z 12 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056631 restraints weight = 21237.616| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.20 r_work: 0.2654 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9385 Z= 0.156 Angle : 0.631 13.009 12686 Z= 0.325 Chirality : 0.040 0.237 1496 Planarity : 0.004 0.041 1618 Dihedral : 7.121 133.588 1369 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 3.69 % Allowed : 15.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.57 (0.23), residues: 1193 helix: 2.70 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -0.29 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 128 TYR 0.016 0.002 TYR E 16 PHE 0.015 0.002 PHE Y 23 TRP 0.010 0.002 TRP C 38 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9385) covalent geometry : angle 0.63080 (12686) hydrogen bonds : bond 0.04705 ( 856) hydrogen bonds : angle 3.70528 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.233 Fit side-chains REVERT: A 17 GLN cc_start: 0.9261 (mt0) cc_final: 0.8788 (mp10) REVERT: A 47 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8304 (tt0) REVERT: A 58 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9008 (mt-10) REVERT: A 60 GLN cc_start: 0.9290 (tt0) cc_final: 0.8871 (tm-30) REVERT: A 64 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7993 (pp20) REVERT: A 86 HIS cc_start: 0.8216 (t70) cc_final: 0.7561 (t70) REVERT: A 92 GLN cc_start: 0.8771 (tp40) cc_final: 0.8401 (tm-30) REVERT: A 94 GLU cc_start: 0.9152 (tp30) cc_final: 0.8657 (tp30) REVERT: A 96 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8403 (pt0) REVERT: A 105 GLU cc_start: 0.8895 (mp0) cc_final: 0.8618 (mp0) REVERT: A 109 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8905 (mt-10) REVERT: A 162 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9090 (p) REVERT: A 223 ASP cc_start: 0.8996 (m-30) cc_final: 0.8699 (m-30) REVERT: B 47 GLU cc_start: 0.9195 (tp30) cc_final: 0.8529 (tp30) REVERT: B 52 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8754 (ttpp) REVERT: B 64 GLU cc_start: 0.8830 (pm20) cc_final: 0.8480 (pm20) REVERT: B 66 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8593 (mmp80) REVERT: B 86 HIS cc_start: 0.8751 (t70) cc_final: 0.8347 (t70) REVERT: B 116 GLU cc_start: 0.9198 (tp30) cc_final: 0.8943 (tp30) REVERT: B 126 MET cc_start: 0.9358 (tpp) cc_final: 0.9126 (mmt) REVERT: B 200 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8403 (mtm180) REVERT: B 223 ASP cc_start: 0.9365 (t70) cc_final: 0.9098 (t0) REVERT: C 18 HIS cc_start: 0.9176 (t70) cc_final: 0.8540 (t-90) REVERT: C 20 ASP cc_start: 0.8468 (t0) cc_final: 0.8267 (t0) REVERT: C 47 GLU cc_start: 0.8888 (tp30) cc_final: 0.8469 (tt0) REVERT: C 64 GLU cc_start: 0.9056 (tp30) cc_final: 0.8266 (tp30) REVERT: C 66 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8801 (mtp85) REVERT: C 72 ASN cc_start: 0.8518 (p0) cc_final: 0.8192 (p0) REVERT: C 93 ASN cc_start: 0.8982 (t0) cc_final: 0.8654 (t0) REVERT: C 94 GLU cc_start: 0.8982 (tp30) cc_final: 0.8151 (tp30) REVERT: C 103 ASP cc_start: 0.8913 (t0) cc_final: 0.8526 (t0) REVERT: C 105 GLU cc_start: 0.8590 (tp30) cc_final: 0.8342 (tp30) REVERT: C 114 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7586 (ttt90) REVERT: C 116 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 161 GLN cc_start: 0.9451 (mt0) cc_final: 0.8871 (mp10) REVERT: C 176 GLU cc_start: 0.9223 (tt0) cc_final: 0.8981 (tt0) REVERT: C 227 GLU cc_start: 0.9382 (tp30) cc_final: 0.8917 (tp30) REVERT: D 13 TRP cc_start: 0.9338 (t-100) cc_final: 0.9120 (t-100) REVERT: D 15 MET cc_start: 0.9342 (mpp) cc_final: 0.8519 (mpp) REVERT: D 18 HIS cc_start: 0.9174 (t70) cc_final: 0.8712 (t70) REVERT: D 50 ASN cc_start: 0.9076 (m-40) cc_final: 0.8783 (m-40) REVERT: D 153 MET cc_start: 0.9066 (ttp) cc_final: 0.8865 (ttm) REVERT: D 223 ASP cc_start: 0.9226 (t0) cc_final: 0.8923 (m-30) REVERT: E 13 TRP cc_start: 0.9116 (t-100) cc_final: 0.8688 (t-100) REVERT: E 47 GLU cc_start: 0.9020 (tp30) cc_final: 0.8808 (tp30) REVERT: E 86 HIS cc_start: 0.8338 (t70) cc_final: 0.8025 (t-90) REVERT: E 94 GLU cc_start: 0.9155 (tp30) cc_final: 0.8570 (tp30) REVERT: E 109 GLU cc_start: 0.9031 (tp30) cc_final: 0.8662 (tp30) REVERT: E 116 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 227 GLU cc_start: 0.9307 (tp30) cc_final: 0.9044 (tp30) REVERT: Z 19 ASN cc_start: 0.9335 (t0) cc_final: 0.9065 (t160) outliers start: 35 outliers final: 9 residues processed: 328 average time/residue: 0.4852 time to fit residues: 170.0290 Evaluate side-chains 310 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 215 GLN B 50 ASN C 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053665 restraints weight = 21394.745| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.23 r_work: 0.2613 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9385 Z= 0.248 Angle : 0.633 9.847 12686 Z= 0.327 Chirality : 0.041 0.255 1496 Planarity : 0.003 0.027 1618 Dihedral : 6.718 129.844 1367 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 5.27 % Allowed : 17.09 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.10 (0.23), residues: 1193 helix: 3.07 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 128 TYR 0.019 0.002 TYR A 195 PHE 0.031 0.002 PHE C 156 TRP 0.013 0.002 TRP C 38 HIS 0.009 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 9385) covalent geometry : angle 0.63298 (12686) hydrogen bonds : bond 0.04532 ( 856) hydrogen bonds : angle 3.65165 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.374 Fit side-chains REVERT: A 17 GLN cc_start: 0.9129 (mt0) cc_final: 0.8763 (mp10) REVERT: A 18 HIS cc_start: 0.8695 (p90) cc_final: 0.8386 (p-80) REVERT: A 47 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8352 (tt0) REVERT: A 60 GLN cc_start: 0.9294 (tt0) cc_final: 0.8926 (tm-30) REVERT: A 64 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8359 (pp20) REVERT: A 86 HIS cc_start: 0.8293 (t70) cc_final: 0.7648 (t70) REVERT: A 92 GLN cc_start: 0.8741 (tp40) cc_final: 0.8180 (tm-30) REVERT: A 94 GLU cc_start: 0.9316 (tp30) cc_final: 0.8827 (tp30) REVERT: A 96 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8448 (mt-10) REVERT: A 103 ASP cc_start: 0.8814 (t0) cc_final: 0.8466 (t0) REVERT: A 109 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8865 (mt-10) REVERT: A 215 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8838 (tt0) REVERT: A 223 ASP cc_start: 0.9008 (m-30) cc_final: 0.8717 (m-30) REVERT: B 24 LYS cc_start: 0.8352 (mttp) cc_final: 0.8124 (mttm) REVERT: B 47 GLU cc_start: 0.9202 (tp30) cc_final: 0.8567 (tp30) REVERT: B 52 LYS cc_start: 0.8995 (ttpp) cc_final: 0.8738 (ttpp) REVERT: B 64 GLU cc_start: 0.8720 (pm20) cc_final: 0.8270 (pm20) REVERT: B 66 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8545 (mmp80) REVERT: B 81 LYS cc_start: 0.9352 (mmmm) cc_final: 0.9138 (mmmm) REVERT: B 86 HIS cc_start: 0.8757 (t70) cc_final: 0.8368 (t70) REVERT: B 116 GLU cc_start: 0.9146 (tp30) cc_final: 0.8867 (tp30) REVERT: B 162 THR cc_start: 0.8868 (t) cc_final: 0.8542 (p) REVERT: B 200 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8247 (ttp-170) REVERT: B 223 ASP cc_start: 0.9380 (t70) cc_final: 0.9100 (t0) REVERT: C 15 MET cc_start: 0.8703 (mtp) cc_final: 0.8501 (mtp) REVERT: C 18 HIS cc_start: 0.9132 (t70) cc_final: 0.8466 (t-90) REVERT: C 20 ASP cc_start: 0.8576 (t0) cc_final: 0.8333 (t0) REVERT: C 47 GLU cc_start: 0.8951 (tp30) cc_final: 0.8413 (tt0) REVERT: C 64 GLU cc_start: 0.9066 (tp30) cc_final: 0.8205 (tp30) REVERT: C 66 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8541 (mtp85) REVERT: C 94 GLU cc_start: 0.9129 (tp30) cc_final: 0.8305 (tp30) REVERT: C 103 ASP cc_start: 0.9010 (t0) cc_final: 0.8620 (t0) REVERT: C 105 GLU cc_start: 0.8696 (tp30) cc_final: 0.8368 (tp30) REVERT: C 114 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7769 (ttt90) REVERT: C 116 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 176 GLU cc_start: 0.9213 (tt0) cc_final: 0.8995 (tt0) REVERT: C 227 GLU cc_start: 0.9414 (tp30) cc_final: 0.8947 (tp30) REVERT: D 15 MET cc_start: 0.9240 (mpp) cc_final: 0.8482 (mpp) REVERT: D 16 TYR cc_start: 0.9177 (t80) cc_final: 0.8962 (t80) REVERT: D 18 HIS cc_start: 0.9201 (t70) cc_final: 0.8722 (t70) REVERT: D 50 ASN cc_start: 0.9063 (m-40) cc_final: 0.8762 (m110) REVERT: D 109 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8759 (mm-30) REVERT: D 223 ASP cc_start: 0.9224 (t0) cc_final: 0.8898 (m-30) REVERT: E 13 TRP cc_start: 0.9124 (t-100) cc_final: 0.8608 (t-100) REVERT: E 86 HIS cc_start: 0.8452 (t70) cc_final: 0.8183 (t-90) REVERT: E 94 GLU cc_start: 0.9340 (tp30) cc_final: 0.8819 (tp30) REVERT: E 206 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8944 (mtmm) REVERT: E 223 ASP cc_start: 0.9073 (m-30) cc_final: 0.8633 (m-30) REVERT: E 227 GLU cc_start: 0.9318 (tp30) cc_final: 0.9021 (tp30) outliers start: 50 outliers final: 15 residues processed: 321 average time/residue: 0.4617 time to fit residues: 158.8480 Evaluate side-chains 310 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN E 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.055245 restraints weight = 21500.332| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.18 r_work: 0.2677 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9385 Z= 0.143 Angle : 0.567 10.066 12686 Z= 0.294 Chirality : 0.038 0.262 1496 Planarity : 0.003 0.032 1618 Dihedral : 6.449 125.399 1367 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.69 % Allowed : 19.09 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.32 (0.23), residues: 1193 helix: 3.23 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.46 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 128 TYR 0.018 0.002 TYR E 16 PHE 0.013 0.001 PHE Z 34 TRP 0.020 0.001 TRP B 13 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9385) covalent geometry : angle 0.56688 (12686) hydrogen bonds : bond 0.04146 ( 856) hydrogen bonds : angle 3.47070 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.262 Fit side-chains REVERT: A 17 GLN cc_start: 0.9085 (mt0) cc_final: 0.8796 (mt0) REVERT: A 18 HIS cc_start: 0.8490 (p90) cc_final: 0.8137 (p-80) REVERT: A 20 ASP cc_start: 0.8510 (t0) cc_final: 0.8291 (t0) REVERT: A 47 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8517 (tt0) REVERT: A 60 GLN cc_start: 0.9292 (tt0) cc_final: 0.8931 (tm-30) REVERT: A 86 HIS cc_start: 0.8364 (t70) cc_final: 0.7719 (t-170) REVERT: A 92 GLN cc_start: 0.8940 (tp40) cc_final: 0.8200 (tm-30) REVERT: A 94 GLU cc_start: 0.9417 (tp30) cc_final: 0.8846 (tp30) REVERT: A 96 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8389 (mt-10) REVERT: A 109 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8958 (mt-10) REVERT: A 223 ASP cc_start: 0.9019 (m-30) cc_final: 0.8747 (m-30) REVERT: B 47 GLU cc_start: 0.9202 (tp30) cc_final: 0.8658 (tm-30) REVERT: B 52 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8894 (ttpp) REVERT: B 58 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9022 (mm-30) REVERT: B 64 GLU cc_start: 0.8786 (pm20) cc_final: 0.8391 (pm20) REVERT: B 66 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8616 (mmp80) REVERT: B 81 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9101 (mmmm) REVERT: B 86 HIS cc_start: 0.8793 (t70) cc_final: 0.8404 (t70) REVERT: B 93 ASN cc_start: 0.9194 (t0) cc_final: 0.8787 (t0) REVERT: B 116 GLU cc_start: 0.9152 (tp30) cc_final: 0.8925 (tp30) REVERT: B 166 ASN cc_start: 0.8602 (t0) cc_final: 0.8333 (t0) REVERT: B 200 ARG cc_start: 0.8851 (tpp-160) cc_final: 0.8355 (ttp-170) REVERT: B 223 ASP cc_start: 0.9347 (t70) cc_final: 0.9041 (t0) REVERT: C 18 HIS cc_start: 0.9054 (t70) cc_final: 0.8343 (t-90) REVERT: C 47 GLU cc_start: 0.9042 (tp30) cc_final: 0.8535 (tt0) REVERT: C 58 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8838 (mm-30) REVERT: C 64 GLU cc_start: 0.9050 (tp30) cc_final: 0.8369 (tp30) REVERT: C 66 ARG cc_start: 0.9095 (mtp85) cc_final: 0.8808 (mtp85) REVERT: C 81 LYS cc_start: 0.9249 (pmtt) cc_final: 0.8956 (pptt) REVERT: C 93 ASN cc_start: 0.9224 (t0) cc_final: 0.8873 (t0) REVERT: C 94 GLU cc_start: 0.9178 (tp30) cc_final: 0.8404 (tp30) REVERT: C 103 ASP cc_start: 0.9071 (t0) cc_final: 0.8739 (t0) REVERT: C 105 GLU cc_start: 0.8742 (tp30) cc_final: 0.8365 (tp30) REVERT: C 114 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7690 (ttt90) REVERT: C 116 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 176 GLU cc_start: 0.9232 (tt0) cc_final: 0.9026 (tt0) REVERT: C 227 GLU cc_start: 0.9407 (tp30) cc_final: 0.8893 (tp30) REVERT: D 15 MET cc_start: 0.9343 (mpp) cc_final: 0.8563 (mpp) REVERT: D 18 HIS cc_start: 0.9110 (t70) cc_final: 0.8574 (t70) REVERT: D 50 ASN cc_start: 0.9222 (m-40) cc_final: 0.8878 (m110) REVERT: D 109 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8817 (mm-30) REVERT: D 223 ASP cc_start: 0.9201 (t0) cc_final: 0.8960 (t0) REVERT: E 13 TRP cc_start: 0.9121 (t-100) cc_final: 0.8653 (t-100) REVERT: E 86 HIS cc_start: 0.8582 (t70) cc_final: 0.8316 (t-90) REVERT: E 94 GLU cc_start: 0.9338 (tp30) cc_final: 0.8906 (tp30) REVERT: E 223 ASP cc_start: 0.9111 (m-30) cc_final: 0.8679 (m-30) REVERT: E 227 GLU cc_start: 0.9327 (tp30) cc_final: 0.9007 (tp30) outliers start: 35 outliers final: 12 residues processed: 325 average time/residue: 0.4670 time to fit residues: 162.5743 Evaluate side-chains 315 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 302 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN D 69 ASN E 50 ASN Z 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.053544 restraints weight = 21381.942| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.28 r_work: 0.2602 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9385 Z= 0.234 Angle : 0.637 10.017 12686 Z= 0.326 Chirality : 0.041 0.262 1496 Planarity : 0.003 0.032 1618 Dihedral : 6.505 121.936 1367 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.90 % Allowed : 20.78 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.23), residues: 1193 helix: 3.21 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.48 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 200 TYR 0.018 0.002 TYR A 195 PHE 0.018 0.002 PHE D 48 TRP 0.024 0.002 TRP B 13 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9385) covalent geometry : angle 0.63658 (12686) hydrogen bonds : bond 0.04282 ( 856) hydrogen bonds : angle 3.56223 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 0.293 Fit side-chains REVERT: A 17 GLN cc_start: 0.9141 (mt0) cc_final: 0.8819 (mt0) REVERT: A 18 HIS cc_start: 0.8717 (p90) cc_final: 0.8385 (p-80) REVERT: A 47 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8314 (tt0) REVERT: A 60 GLN cc_start: 0.9292 (tt0) cc_final: 0.8934 (tm-30) REVERT: A 64 GLU cc_start: 0.8506 (pp20) cc_final: 0.8267 (pp20) REVERT: A 86 HIS cc_start: 0.8211 (t70) cc_final: 0.7538 (t70) REVERT: A 92 GLN cc_start: 0.8669 (tp40) cc_final: 0.7969 (tm-30) REVERT: A 94 GLU cc_start: 0.9348 (tp30) cc_final: 0.8735 (tp30) REVERT: A 96 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 109 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8846 (mt-10) REVERT: A 223 ASP cc_start: 0.8986 (m-30) cc_final: 0.8657 (m-30) REVERT: B 24 LYS cc_start: 0.8268 (mttp) cc_final: 0.8051 (mttm) REVERT: B 47 GLU cc_start: 0.9181 (tp30) cc_final: 0.8588 (tm-30) REVERT: B 52 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8733 (ttpp) REVERT: B 64 GLU cc_start: 0.8696 (pm20) cc_final: 0.8423 (pm20) REVERT: B 66 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8586 (mmp80) REVERT: B 81 LYS cc_start: 0.9378 (mmmm) cc_final: 0.9098 (mmmm) REVERT: B 86 HIS cc_start: 0.8749 (t70) cc_final: 0.8345 (t70) REVERT: B 103 ASP cc_start: 0.8764 (t0) cc_final: 0.8250 (t0) REVERT: B 105 GLU cc_start: 0.8897 (mp0) cc_final: 0.8557 (pm20) REVERT: B 116 GLU cc_start: 0.9132 (tp30) cc_final: 0.8854 (tp30) REVERT: B 162 THR cc_start: 0.8671 (t) cc_final: 0.8330 (p) REVERT: B 166 ASN cc_start: 0.8485 (t0) cc_final: 0.8160 (t0) REVERT: B 200 ARG cc_start: 0.8816 (tpp-160) cc_final: 0.8329 (ttm170) REVERT: B 223 ASP cc_start: 0.9373 (t70) cc_final: 0.9089 (t0) REVERT: C 15 MET cc_start: 0.8675 (mtp) cc_final: 0.8358 (mtp) REVERT: C 18 HIS cc_start: 0.9117 (t70) cc_final: 0.8386 (t-90) REVERT: C 47 GLU cc_start: 0.8963 (tp30) cc_final: 0.8410 (tt0) REVERT: C 58 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8708 (mm-30) REVERT: C 64 GLU cc_start: 0.9067 (tp30) cc_final: 0.8293 (tp30) REVERT: C 66 ARG cc_start: 0.9073 (mtp85) cc_final: 0.8713 (mtp85) REVERT: C 72 ASN cc_start: 0.8303 (p0) cc_final: 0.8052 (p0) REVERT: C 81 LYS cc_start: 0.9276 (pmtt) cc_final: 0.9013 (pptt) REVERT: C 93 ASN cc_start: 0.8973 (t0) cc_final: 0.8641 (t0) REVERT: C 94 GLU cc_start: 0.9161 (tp30) cc_final: 0.8203 (tp30) REVERT: C 103 ASP cc_start: 0.9025 (t0) cc_final: 0.8256 (t0) REVERT: C 114 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7569 (ttt90) REVERT: C 116 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 176 GLU cc_start: 0.9154 (tt0) cc_final: 0.8948 (tt0) REVERT: C 227 GLU cc_start: 0.9400 (tp30) cc_final: 0.8939 (tp30) REVERT: D 15 MET cc_start: 0.9199 (mpp) cc_final: 0.8475 (mpp) REVERT: D 18 HIS cc_start: 0.9086 (t70) cc_final: 0.8562 (t70) REVERT: D 50 ASN cc_start: 0.9071 (m-40) cc_final: 0.8771 (m110) REVERT: D 109 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8807 (mm-30) REVERT: D 223 ASP cc_start: 0.9214 (t0) cc_final: 0.8875 (m-30) REVERT: E 13 TRP cc_start: 0.9104 (t-100) cc_final: 0.8586 (t-100) REVERT: E 58 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8756 (mm-30) REVERT: E 86 HIS cc_start: 0.8438 (t70) cc_final: 0.8209 (t-90) REVERT: E 94 GLU cc_start: 0.9402 (tp30) cc_final: 0.8889 (tp30) REVERT: E 223 ASP cc_start: 0.9080 (m-30) cc_final: 0.8628 (m-30) REVERT: E 227 GLU cc_start: 0.9309 (tp30) cc_final: 0.9001 (tp30) REVERT: Z 35 MET cc_start: 0.8623 (tpp) cc_final: 0.7802 (mpp) outliers start: 37 outliers final: 18 residues processed: 326 average time/residue: 0.4832 time to fit residues: 168.6805 Evaluate side-chains 320 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN B 161 GLN E 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055022 restraints weight = 21287.363| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.20 r_work: 0.2631 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9385 Z= 0.177 Angle : 0.616 10.831 12686 Z= 0.316 Chirality : 0.040 0.276 1496 Planarity : 0.003 0.038 1618 Dihedral : 6.420 120.151 1367 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.48 % Allowed : 23.21 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.23), residues: 1193 helix: 3.24 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.52 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 118 TYR 0.022 0.002 TYR A 16 PHE 0.016 0.001 PHE D 48 TRP 0.028 0.002 TRP B 13 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9385) covalent geometry : angle 0.61650 (12686) hydrogen bonds : bond 0.04127 ( 856) hydrogen bonds : angle 3.51174 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 0.235 Fit side-chains REVERT: A 17 GLN cc_start: 0.9115 (mt0) cc_final: 0.8796 (mt0) REVERT: A 18 HIS cc_start: 0.8681 (p90) cc_final: 0.8418 (p-80) REVERT: A 47 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8373 (tt0) REVERT: A 60 GLN cc_start: 0.9303 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 64 GLU cc_start: 0.8549 (pp20) cc_final: 0.8266 (pp20) REVERT: A 86 HIS cc_start: 0.8184 (t70) cc_final: 0.7625 (t70) REVERT: A 92 GLN cc_start: 0.8687 (tp40) cc_final: 0.8017 (tm-30) REVERT: A 94 GLU cc_start: 0.9366 (tp30) cc_final: 0.8805 (tp30) REVERT: A 96 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 109 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8848 (mt-10) REVERT: A 223 ASP cc_start: 0.9010 (m-30) cc_final: 0.8694 (m-30) REVERT: B 15 MET cc_start: 0.9387 (mtp) cc_final: 0.9170 (mtp) REVERT: B 24 LYS cc_start: 0.8333 (mttp) cc_final: 0.8088 (mttm) REVERT: B 47 GLU cc_start: 0.9196 (tp30) cc_final: 0.8612 (tm-30) REVERT: B 52 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8772 (ttpp) REVERT: B 64 GLU cc_start: 0.8702 (pm20) cc_final: 0.8442 (pm20) REVERT: B 66 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8578 (mmp80) REVERT: B 81 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9114 (mmmm) REVERT: B 86 HIS cc_start: 0.8756 (t70) cc_final: 0.8342 (t70) REVERT: B 105 GLU cc_start: 0.8905 (mp0) cc_final: 0.8564 (pm20) REVERT: B 116 GLU cc_start: 0.9111 (tp30) cc_final: 0.8855 (tp30) REVERT: B 162 THR cc_start: 0.8635 (t) cc_final: 0.8274 (p) REVERT: B 166 ASN cc_start: 0.8528 (t0) cc_final: 0.8185 (t0) REVERT: B 200 ARG cc_start: 0.8798 (tpp-160) cc_final: 0.8230 (ttp-170) REVERT: B 223 ASP cc_start: 0.9365 (t70) cc_final: 0.9070 (t0) REVERT: C 15 MET cc_start: 0.8684 (mtp) cc_final: 0.8396 (mtp) REVERT: C 18 HIS cc_start: 0.9061 (t70) cc_final: 0.8312 (t-90) REVERT: C 52 LYS cc_start: 0.8988 (tptm) cc_final: 0.8728 (tptt) REVERT: C 64 GLU cc_start: 0.9071 (tp30) cc_final: 0.8310 (tp30) REVERT: C 66 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8710 (mtp85) REVERT: C 72 ASN cc_start: 0.8319 (p0) cc_final: 0.8055 (p0) REVERT: C 81 LYS cc_start: 0.9247 (pmtt) cc_final: 0.9006 (pptt) REVERT: C 93 ASN cc_start: 0.8970 (t0) cc_final: 0.8664 (t0) REVERT: C 114 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7846 (ttt90) REVERT: C 116 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8441 (tm-30) REVERT: C 176 GLU cc_start: 0.9125 (tt0) cc_final: 0.8899 (tt0) REVERT: C 227 GLU cc_start: 0.9422 (tp30) cc_final: 0.9023 (tp30) REVERT: D 15 MET cc_start: 0.9227 (mpp) cc_final: 0.8526 (mpp) REVERT: D 18 HIS cc_start: 0.9053 (t70) cc_final: 0.8511 (t70) REVERT: D 50 ASN cc_start: 0.9106 (m-40) cc_final: 0.8793 (m110) REVERT: D 109 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8805 (mm-30) REVERT: D 223 ASP cc_start: 0.9194 (t0) cc_final: 0.8968 (t0) REVERT: E 13 TRP cc_start: 0.9095 (t-100) cc_final: 0.8611 (t-100) REVERT: E 58 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8740 (mm-30) REVERT: E 81 LYS cc_start: 0.9541 (mtmm) cc_final: 0.9309 (mmmm) REVERT: E 86 HIS cc_start: 0.8462 (t70) cc_final: 0.8186 (t-90) REVERT: E 94 GLU cc_start: 0.9397 (tp30) cc_final: 0.8914 (tp30) REVERT: E 109 GLU cc_start: 0.9042 (tp30) cc_final: 0.8582 (tp30) REVERT: E 116 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8743 (tm-30) REVERT: E 223 ASP cc_start: 0.9098 (m-30) cc_final: 0.8643 (m-30) REVERT: E 227 GLU cc_start: 0.9324 (tp30) cc_final: 0.9050 (tp30) outliers start: 33 outliers final: 21 residues processed: 317 average time/residue: 0.4724 time to fit residues: 160.2668 Evaluate side-chains 318 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN D 69 ASN E 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056350 restraints weight = 21142.765| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.22 r_work: 0.2690 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9385 Z= 0.146 Angle : 0.637 11.591 12686 Z= 0.323 Chirality : 0.040 0.294 1496 Planarity : 0.003 0.043 1618 Dihedral : 6.310 117.348 1367 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.95 % Allowed : 24.47 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.27 (0.23), residues: 1193 helix: 3.21 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.56 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 200 TYR 0.017 0.001 TYR A 195 PHE 0.017 0.001 PHE Z 34 TRP 0.032 0.002 TRP B 13 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9385) covalent geometry : angle 0.63689 (12686) hydrogen bonds : bond 0.03958 ( 856) hydrogen bonds : angle 3.46088 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.404 Fit side-chains REVERT: A 17 GLN cc_start: 0.9116 (mt0) cc_final: 0.8777 (mt0) REVERT: A 18 HIS cc_start: 0.8676 (p90) cc_final: 0.8366 (p-80) REVERT: A 47 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8364 (tt0) REVERT: A 60 GLN cc_start: 0.9280 (tt0) cc_final: 0.8920 (tm-30) REVERT: A 64 GLU cc_start: 0.8568 (pp20) cc_final: 0.8245 (pp20) REVERT: A 86 HIS cc_start: 0.8214 (t70) cc_final: 0.7754 (t70) REVERT: A 89 ASN cc_start: 0.9002 (m-40) cc_final: 0.8619 (m110) REVERT: A 92 GLN cc_start: 0.8649 (tp40) cc_final: 0.8117 (tm-30) REVERT: A 94 GLU cc_start: 0.9336 (tp30) cc_final: 0.8759 (tp30) REVERT: A 96 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 109 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8811 (mt-10) REVERT: A 223 ASP cc_start: 0.9010 (m-30) cc_final: 0.8689 (m-30) REVERT: B 47 GLU cc_start: 0.9196 (tp30) cc_final: 0.8619 (tm-30) REVERT: B 52 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8752 (ttpp) REVERT: B 64 GLU cc_start: 0.8695 (pm20) cc_final: 0.8430 (pm20) REVERT: B 66 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8617 (mmp80) REVERT: B 81 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9110 (mmmm) REVERT: B 86 HIS cc_start: 0.8743 (t70) cc_final: 0.8456 (t70) REVERT: B 103 ASP cc_start: 0.8691 (t0) cc_final: 0.8190 (t0) REVERT: B 105 GLU cc_start: 0.8876 (mp0) cc_final: 0.8546 (pm20) REVERT: B 116 GLU cc_start: 0.9042 (tp30) cc_final: 0.8803 (tp30) REVERT: B 166 ASN cc_start: 0.8552 (t0) cc_final: 0.8221 (t0) REVERT: B 200 ARG cc_start: 0.8807 (tpp-160) cc_final: 0.8255 (ttp-170) REVERT: B 223 ASP cc_start: 0.9355 (t70) cc_final: 0.9064 (t0) REVERT: C 15 MET cc_start: 0.8698 (mtp) cc_final: 0.8403 (mtp) REVERT: C 18 HIS cc_start: 0.9057 (t70) cc_final: 0.8275 (t-90) REVERT: C 47 GLU cc_start: 0.8917 (tp30) cc_final: 0.8507 (tt0) REVERT: C 58 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8809 (mm-30) REVERT: C 64 GLU cc_start: 0.9052 (tp30) cc_final: 0.8340 (tp30) REVERT: C 66 ARG cc_start: 0.9034 (mtp85) cc_final: 0.8687 (mtp85) REVERT: C 72 ASN cc_start: 0.8296 (p0) cc_final: 0.8012 (p0) REVERT: C 81 LYS cc_start: 0.9218 (pmtt) cc_final: 0.9017 (pptt) REVERT: C 93 ASN cc_start: 0.8993 (t0) cc_final: 0.8679 (t0) REVERT: C 94 GLU cc_start: 0.9104 (tp30) cc_final: 0.8659 (tp30) REVERT: C 103 ASP cc_start: 0.8923 (t0) cc_final: 0.8473 (t0) REVERT: C 109 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8731 (tp30) REVERT: C 116 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 176 GLU cc_start: 0.9132 (tt0) cc_final: 0.8923 (tt0) REVERT: C 227 GLU cc_start: 0.9418 (tp30) cc_final: 0.8923 (tp30) REVERT: D 15 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8584 (mpp) REVERT: D 18 HIS cc_start: 0.9032 (t70) cc_final: 0.8394 (t70) REVERT: D 50 ASN cc_start: 0.9092 (m-40) cc_final: 0.8767 (m110) REVERT: D 109 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8814 (mm-30) REVERT: D 223 ASP cc_start: 0.9177 (t0) cc_final: 0.8969 (t0) REVERT: E 13 TRP cc_start: 0.9076 (t-100) cc_final: 0.8619 (t-100) REVERT: E 24 LYS cc_start: 0.8665 (mttp) cc_final: 0.8403 (mttm) REVERT: E 58 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8724 (mm-30) REVERT: E 81 LYS cc_start: 0.9521 (mtmm) cc_final: 0.9278 (mmmm) REVERT: E 86 HIS cc_start: 0.8430 (t70) cc_final: 0.8113 (t-170) REVERT: E 94 GLU cc_start: 0.9374 (tp30) cc_final: 0.8922 (tp30) REVERT: E 109 GLU cc_start: 0.9012 (tp30) cc_final: 0.8515 (tp30) REVERT: E 116 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8729 (tm-30) REVERT: E 153 MET cc_start: 0.8894 (ttm) cc_final: 0.8550 (ttm) REVERT: E 223 ASP cc_start: 0.9078 (m-30) cc_final: 0.8625 (m-30) REVERT: E 227 GLU cc_start: 0.9322 (tp30) cc_final: 0.9042 (tp30) REVERT: Z 35 MET cc_start: 0.8622 (tpp) cc_final: 0.7929 (mpp) outliers start: 28 outliers final: 17 residues processed: 327 average time/residue: 0.5566 time to fit residues: 195.0382 Evaluate side-chains 320 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN C 154 ASN E 50 ASN E 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.055823 restraints weight = 21353.726| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.20 r_work: 0.2654 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9385 Z= 0.173 Angle : 0.664 11.450 12686 Z= 0.335 Chirality : 0.042 0.302 1496 Planarity : 0.003 0.048 1618 Dihedral : 6.293 116.482 1367 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.85 % Allowed : 26.48 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.24), residues: 1193 helix: 3.23 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.55 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 200 TYR 0.020 0.002 TYR A 16 PHE 0.017 0.001 PHE A 156 TRP 0.035 0.002 TRP B 13 HIS 0.002 0.000 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9385) covalent geometry : angle 0.66433 (12686) hydrogen bonds : bond 0.03987 ( 856) hydrogen bonds : angle 3.50596 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.366 Fit side-chains REVERT: A 17 GLN cc_start: 0.9124 (mt0) cc_final: 0.8811 (mt0) REVERT: A 18 HIS cc_start: 0.8670 (p90) cc_final: 0.8389 (p-80) REVERT: A 47 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8403 (tt0) REVERT: A 60 GLN cc_start: 0.9276 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 64 GLU cc_start: 0.8592 (pp20) cc_final: 0.8258 (pp20) REVERT: A 86 HIS cc_start: 0.8300 (t70) cc_final: 0.7741 (t70) REVERT: A 89 ASN cc_start: 0.9032 (m-40) cc_final: 0.8648 (m110) REVERT: A 92 GLN cc_start: 0.8680 (tp40) cc_final: 0.8099 (tm-30) REVERT: A 94 GLU cc_start: 0.9366 (tp30) cc_final: 0.8746 (tp30) REVERT: A 96 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 109 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8836 (mt-10) REVERT: A 223 ASP cc_start: 0.9014 (m-30) cc_final: 0.8696 (m-30) REVERT: B 47 GLU cc_start: 0.9193 (tp30) cc_final: 0.8613 (tm-30) REVERT: B 52 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8776 (ttpp) REVERT: B 64 GLU cc_start: 0.8717 (pm20) cc_final: 0.8428 (pm20) REVERT: B 66 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8628 (mmp80) REVERT: B 69 ASN cc_start: 0.8979 (m-40) cc_final: 0.8612 (m-40) REVERT: B 81 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9116 (mmmm) REVERT: B 86 HIS cc_start: 0.8767 (t70) cc_final: 0.8536 (t70) REVERT: B 103 ASP cc_start: 0.8712 (t0) cc_final: 0.8032 (t0) REVERT: B 105 GLU cc_start: 0.8911 (mp0) cc_final: 0.8565 (pm20) REVERT: B 116 GLU cc_start: 0.9059 (tp30) cc_final: 0.8800 (tp30) REVERT: B 162 THR cc_start: 0.8576 (t) cc_final: 0.8248 (p) REVERT: B 166 ASN cc_start: 0.8591 (t0) cc_final: 0.8263 (t0) REVERT: B 200 ARG cc_start: 0.8829 (tpp-160) cc_final: 0.8258 (ttp-170) REVERT: B 223 ASP cc_start: 0.9346 (t70) cc_final: 0.9041 (t0) REVERT: C 15 MET cc_start: 0.8721 (mtp) cc_final: 0.8477 (mtp) REVERT: C 18 HIS cc_start: 0.9049 (t70) cc_final: 0.8329 (t-90) REVERT: C 47 GLU cc_start: 0.8952 (tp30) cc_final: 0.8495 (tt0) REVERT: C 58 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8825 (mm-30) REVERT: C 64 GLU cc_start: 0.9071 (tp30) cc_final: 0.8522 (tm-30) REVERT: C 72 ASN cc_start: 0.8308 (p0) cc_final: 0.8024 (p0) REVERT: C 81 LYS cc_start: 0.9218 (pmtt) cc_final: 0.9018 (pptt) REVERT: C 93 ASN cc_start: 0.8962 (t0) cc_final: 0.8647 (t0) REVERT: C 94 GLU cc_start: 0.9151 (tp30) cc_final: 0.8610 (tp30) REVERT: C 103 ASP cc_start: 0.8593 (t0) cc_final: 0.8385 (t0) REVERT: C 176 GLU cc_start: 0.9150 (tt0) cc_final: 0.8947 (tt0) REVERT: C 227 GLU cc_start: 0.9434 (tp30) cc_final: 0.8949 (tp30) REVERT: D 15 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8595 (mpp) REVERT: D 18 HIS cc_start: 0.9039 (t70) cc_final: 0.8444 (t70) REVERT: D 50 ASN cc_start: 0.9108 (m-40) cc_final: 0.8794 (m110) REVERT: D 109 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8831 (mm-30) REVERT: D 223 ASP cc_start: 0.9181 (t0) cc_final: 0.8970 (t0) REVERT: E 13 TRP cc_start: 0.9041 (t-100) cc_final: 0.8526 (t-100) REVERT: E 16 TYR cc_start: 0.9246 (t80) cc_final: 0.9041 (t80) REVERT: E 24 LYS cc_start: 0.8659 (mttp) cc_final: 0.8366 (mttm) REVERT: E 81 LYS cc_start: 0.9529 (mtmm) cc_final: 0.9290 (mmmm) REVERT: E 86 HIS cc_start: 0.8402 (t70) cc_final: 0.8158 (t-170) REVERT: E 94 GLU cc_start: 0.9413 (tp30) cc_final: 0.8958 (tp30) REVERT: E 109 GLU cc_start: 0.9019 (tp30) cc_final: 0.8589 (tp30) REVERT: E 116 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8743 (tm-30) REVERT: E 153 MET cc_start: 0.8959 (ttm) cc_final: 0.8634 (ttm) REVERT: E 223 ASP cc_start: 0.9095 (m-30) cc_final: 0.8651 (m-30) REVERT: E 227 GLU cc_start: 0.9326 (tp30) cc_final: 0.9047 (tp30) REVERT: Z 35 MET cc_start: 0.8498 (tpp) cc_final: 0.7791 (mpp) outliers start: 27 outliers final: 19 residues processed: 312 average time/residue: 0.5413 time to fit residues: 180.9478 Evaluate side-chains 318 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 298 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN D 69 ASN E 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057140 restraints weight = 21147.998| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.18 r_work: 0.2671 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9385 Z= 0.155 Angle : 0.677 15.521 12686 Z= 0.340 Chirality : 0.042 0.332 1496 Planarity : 0.003 0.049 1618 Dihedral : 6.239 114.280 1367 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.53 % Allowed : 27.00 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.24), residues: 1193 helix: 3.23 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.51 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 200 TYR 0.018 0.001 TYR A 195 PHE 0.026 0.001 PHE A 156 TRP 0.040 0.002 TRP B 13 HIS 0.002 0.000 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9385) covalent geometry : angle 0.67714 (12686) hydrogen bonds : bond 0.03900 ( 856) hydrogen bonds : angle 3.48529 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.407 Fit side-chains REVERT: A 17 GLN cc_start: 0.9135 (mt0) cc_final: 0.8808 (mt0) REVERT: A 18 HIS cc_start: 0.8650 (p90) cc_final: 0.8379 (p-80) REVERT: A 47 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8398 (tt0) REVERT: A 60 GLN cc_start: 0.9277 (tt0) cc_final: 0.8919 (tm-30) REVERT: A 64 GLU cc_start: 0.8610 (pp20) cc_final: 0.8269 (pp20) REVERT: A 86 HIS cc_start: 0.8273 (t70) cc_final: 0.7686 (t70) REVERT: A 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8652 (m110) REVERT: A 92 GLN cc_start: 0.8678 (tp40) cc_final: 0.8107 (tm-30) REVERT: A 94 GLU cc_start: 0.9370 (tp30) cc_final: 0.8791 (tp30) REVERT: A 96 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 105 GLU cc_start: 0.8828 (mp0) cc_final: 0.8592 (mp0) REVERT: A 109 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 223 ASP cc_start: 0.9022 (m-30) cc_final: 0.8702 (m-30) REVERT: B 47 GLU cc_start: 0.9188 (tp30) cc_final: 0.8610 (tm-30) REVERT: B 52 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8764 (ttpp) REVERT: B 64 GLU cc_start: 0.8702 (pm20) cc_final: 0.8411 (pm20) REVERT: B 66 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8613 (mmp80) REVERT: B 81 LYS cc_start: 0.9378 (mmmm) cc_final: 0.9134 (mmmm) REVERT: B 86 HIS cc_start: 0.8809 (t70) cc_final: 0.8474 (t70) REVERT: B 93 ASN cc_start: 0.8967 (t0) cc_final: 0.8661 (t0) REVERT: B 103 ASP cc_start: 0.8566 (t0) cc_final: 0.7992 (t0) REVERT: B 105 GLU cc_start: 0.8892 (mp0) cc_final: 0.8552 (pm20) REVERT: B 116 GLU cc_start: 0.9068 (tp30) cc_final: 0.8813 (tp30) REVERT: B 162 THR cc_start: 0.8464 (t) cc_final: 0.8128 (p) REVERT: B 166 ASN cc_start: 0.8581 (t0) cc_final: 0.8261 (t0) REVERT: B 200 ARG cc_start: 0.8833 (tpp-160) cc_final: 0.8261 (ttp-170) REVERT: B 223 ASP cc_start: 0.9347 (t70) cc_final: 0.9042 (t0) REVERT: C 15 MET cc_start: 0.8835 (mtp) cc_final: 0.8479 (mtp) REVERT: C 18 HIS cc_start: 0.9017 (t70) cc_final: 0.8298 (t-90) REVERT: C 47 GLU cc_start: 0.8963 (tp30) cc_final: 0.8499 (tt0) REVERT: C 52 LYS cc_start: 0.9014 (tptm) cc_final: 0.8792 (tptt) REVERT: C 58 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8857 (mm-30) REVERT: C 64 GLU cc_start: 0.9056 (tp30) cc_final: 0.8525 (tm-30) REVERT: C 72 ASN cc_start: 0.8293 (p0) cc_final: 0.8007 (p0) REVERT: C 93 ASN cc_start: 0.8967 (t0) cc_final: 0.8639 (t0) REVERT: C 94 GLU cc_start: 0.9145 (tp30) cc_final: 0.8597 (tp30) REVERT: C 227 GLU cc_start: 0.9433 (tp30) cc_final: 0.8956 (tp30) REVERT: D 15 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8574 (mpp) REVERT: D 18 HIS cc_start: 0.9012 (t70) cc_final: 0.8356 (t70) REVERT: D 50 ASN cc_start: 0.9105 (m-40) cc_final: 0.8798 (m110) REVERT: D 109 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8770 (mm-30) REVERT: D 223 ASP cc_start: 0.9176 (t0) cc_final: 0.8963 (t0) REVERT: E 13 TRP cc_start: 0.9036 (t-100) cc_final: 0.8565 (t-100) REVERT: E 24 LYS cc_start: 0.8676 (mttp) cc_final: 0.8373 (mttm) REVERT: E 58 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8733 (mm-30) REVERT: E 81 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9277 (mmmm) REVERT: E 86 HIS cc_start: 0.8399 (t70) cc_final: 0.7968 (t-170) REVERT: E 94 GLU cc_start: 0.9407 (tp30) cc_final: 0.8967 (tp30) REVERT: E 109 GLU cc_start: 0.9009 (tp30) cc_final: 0.8652 (tp30) REVERT: E 153 MET cc_start: 0.8969 (ttm) cc_final: 0.8652 (ttm) REVERT: E 223 ASP cc_start: 0.9074 (m-30) cc_final: 0.8627 (m-30) REVERT: E 227 GLU cc_start: 0.9322 (tp30) cc_final: 0.9040 (tp30) REVERT: Z 35 MET cc_start: 0.8459 (tpp) cc_final: 0.7824 (mpp) outliers start: 24 outliers final: 21 residues processed: 318 average time/residue: 0.5452 time to fit residues: 185.9199 Evaluate side-chains 327 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN C 104 ASN E 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056879 restraints weight = 21204.052| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.20 r_work: 0.2678 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9385 Z= 0.160 Angle : 0.694 15.159 12686 Z= 0.348 Chirality : 0.042 0.336 1496 Planarity : 0.003 0.056 1618 Dihedral : 6.223 113.339 1367 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.32 % Allowed : 27.74 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.24), residues: 1193 helix: 3.22 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.50 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 200 TYR 0.021 0.002 TYR A 16 PHE 0.016 0.001 PHE D 48 TRP 0.043 0.002 TRP D 13 HIS 0.002 0.000 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9385) covalent geometry : angle 0.69359 (12686) hydrogen bonds : bond 0.03894 ( 856) hydrogen bonds : angle 3.48846 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 0.369 Fit side-chains REVERT: A 17 GLN cc_start: 0.9131 (mt0) cc_final: 0.8809 (mt0) REVERT: A 18 HIS cc_start: 0.8674 (p90) cc_final: 0.8402 (p-80) REVERT: A 47 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8403 (tt0) REVERT: A 60 GLN cc_start: 0.9267 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 64 GLU cc_start: 0.8608 (pp20) cc_final: 0.8243 (pp20) REVERT: A 86 HIS cc_start: 0.8256 (t70) cc_final: 0.7744 (t70) REVERT: A 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8632 (m110) REVERT: A 92 GLN cc_start: 0.8687 (tp40) cc_final: 0.8109 (tm-30) REVERT: A 94 GLU cc_start: 0.9373 (tp30) cc_final: 0.8768 (tp30) REVERT: A 96 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8409 (mt-10) REVERT: A 223 ASP cc_start: 0.9020 (m-30) cc_final: 0.8697 (m-30) REVERT: B 47 GLU cc_start: 0.9186 (tp30) cc_final: 0.8605 (tm-30) REVERT: B 52 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8759 (ttpp) REVERT: B 64 GLU cc_start: 0.8683 (pm20) cc_final: 0.8398 (pm20) REVERT: B 66 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8619 (mmp80) REVERT: B 81 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9136 (mmmm) REVERT: B 86 HIS cc_start: 0.8766 (t70) cc_final: 0.8470 (t70) REVERT: B 93 ASN cc_start: 0.8960 (t0) cc_final: 0.8656 (t0) REVERT: B 103 ASP cc_start: 0.8566 (t0) cc_final: 0.7983 (t0) REVERT: B 105 GLU cc_start: 0.8901 (mp0) cc_final: 0.8566 (pm20) REVERT: B 116 GLU cc_start: 0.9044 (tp30) cc_final: 0.8780 (tp30) REVERT: B 162 THR cc_start: 0.8391 (t) cc_final: 0.8032 (p) REVERT: B 166 ASN cc_start: 0.8573 (t0) cc_final: 0.8248 (t0) REVERT: B 200 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8254 (ttp-170) REVERT: B 223 ASP cc_start: 0.9344 (t70) cc_final: 0.9038 (t0) REVERT: C 16 TYR cc_start: 0.9131 (t80) cc_final: 0.8891 (t80) REVERT: C 18 HIS cc_start: 0.9148 (t70) cc_final: 0.8559 (t-90) REVERT: C 47 GLU cc_start: 0.8954 (tp30) cc_final: 0.8494 (tt0) REVERT: C 52 LYS cc_start: 0.9025 (tptm) cc_final: 0.8791 (tptt) REVERT: C 58 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8852 (mm-30) REVERT: C 64 GLU cc_start: 0.9056 (tp30) cc_final: 0.8519 (tm-30) REVERT: C 72 ASN cc_start: 0.8286 (p0) cc_final: 0.8019 (p0) REVERT: C 93 ASN cc_start: 0.8963 (t0) cc_final: 0.8629 (t0) REVERT: C 94 GLU cc_start: 0.9145 (tp30) cc_final: 0.8499 (tp30) REVERT: C 227 GLU cc_start: 0.9429 (tp30) cc_final: 0.8957 (tp30) REVERT: D 15 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8562 (mpp) REVERT: D 18 HIS cc_start: 0.9029 (t70) cc_final: 0.8391 (t70) REVERT: D 50 ASN cc_start: 0.9108 (m-40) cc_final: 0.8799 (m110) REVERT: D 109 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8820 (mm-30) REVERT: D 223 ASP cc_start: 0.9172 (t0) cc_final: 0.8957 (t0) REVERT: E 13 TRP cc_start: 0.9036 (t-100) cc_final: 0.8539 (t-100) REVERT: E 24 LYS cc_start: 0.8660 (mttp) cc_final: 0.8365 (mttm) REVERT: E 58 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8742 (mm-30) REVERT: E 81 LYS cc_start: 0.9507 (mtmm) cc_final: 0.9274 (mmmm) REVERT: E 86 HIS cc_start: 0.8415 (t70) cc_final: 0.8023 (t-170) REVERT: E 94 GLU cc_start: 0.9408 (tp30) cc_final: 0.8972 (tp30) REVERT: E 109 GLU cc_start: 0.9016 (tp30) cc_final: 0.8586 (tp30) REVERT: E 116 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8738 (tm-30) REVERT: E 153 MET cc_start: 0.8969 (ttm) cc_final: 0.8641 (ttm) REVERT: E 223 ASP cc_start: 0.9078 (m-30) cc_final: 0.8631 (m-30) REVERT: E 227 GLU cc_start: 0.9323 (tp30) cc_final: 0.9040 (tp30) REVERT: Z 35 MET cc_start: 0.8424 (tpp) cc_final: 0.7863 (mpp) outliers start: 22 outliers final: 16 residues processed: 315 average time/residue: 0.5470 time to fit residues: 184.5747 Evaluate side-chains 321 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 304 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Z residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 27 optimal weight: 0.0000 chunk 16 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 50 ASN D 69 ASN E 50 ASN E 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057257 restraints weight = 21006.035| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.19 r_work: 0.2714 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 9385 Z= 0.157 Angle : 0.713 15.396 12686 Z= 0.362 Chirality : 0.042 0.341 1496 Planarity : 0.003 0.055 1618 Dihedral : 6.159 112.083 1367 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.22 % Allowed : 27.64 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.33 (0.24), residues: 1193 helix: 3.24 (0.15), residues: 1047 sheet: None (None), residues: 0 loop : -0.47 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 200 TYR 0.017 0.001 TYR A 195 PHE 0.022 0.001 PHE Z 34 TRP 0.045 0.002 TRP B 13 HIS 0.002 0.000 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9385) covalent geometry : angle 0.71263 (12686) hydrogen bonds : bond 0.03865 ( 856) hydrogen bonds : angle 3.49427 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.30 seconds wall clock time: 62 minutes 36.36 seconds (3756.36 seconds total)