Starting phenix.real_space_refine on Sun Jul 27 06:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddo_46778/07_2025/9ddo_46778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddo_46778/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ddo_46778/07_2025/9ddo_46778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddo_46778/07_2025/9ddo_46778.map" model { file = "/net/cci-nas-00/data/ceres_data/9ddo_46778/07_2025/9ddo_46778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddo_46778/07_2025/9ddo_46778.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.00, per 1000 atoms: 0.65 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.65 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: 2.61 Time building geometry restraints manager: 2.74 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: 1.030 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.780 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (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 TRP 0.088 0.015 TRP B 13 HIS 0.013 0.002 HIS F 20 PHE 0.117 0.010 PHE Y 23 TYR 0.104 0.022 TYR A 16 ARG 0.006 0.001 ARG D 222 Details of bonding type rmsd hydrogen bonds : bond 0.15129 ( 856) hydrogen bonds : angle 6.19296 ( 2565) covalent geometry : bond 0.01108 ( 9385) covalent geometry : angle 1.61410 (12686) *********************** 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 : 1.203 Fit side-chains revert: symmetry clash REVERT: A 13 TRP cc_start: 0.9323 (t-100) cc_final: 0.8678 (t-100) REVERT: A 17 GLN cc_start: 0.9120 (mt0) cc_final: 0.8668 (mm110) REVERT: A 18 HIS cc_start: 0.7952 (p-80) cc_final: 0.7578 (p-80) REVERT: A 58 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8803 (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: 0.7608 (t70) REVERT: A 90 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8551 (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: 0.8458 (tp30) REVERT: B 52 LYS cc_start: 0.9252 (ttpp) cc_final: 0.8954 (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: 0.8556 (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 58 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8480 (mt-10) 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: 0.9123 (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 223 ASP cc_start: 0.9110 (t0) cc_final: 0.8843 (t0) REVERT: D 227 GLU cc_start: 0.9054 (tp30) cc_final: 0.8622 (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: 0.7994 (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: 1.6178 time to fit residues: 658.0064 Evaluate side-chains 302 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.073108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056427 restraints weight = 20950.251| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.22 r_work: 0.2669 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2496 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= 0.154 Angle : 0.626 12.742 12686 Z= 0.325 Chirality : 0.040 0.233 1496 Planarity : 0.004 0.040 1618 Dihedral : 7.122 133.381 1369 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 3.48 % Allowed : 15.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.23), residues: 1193 helix: 2.69 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -0.24 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 38 HIS 0.005 0.001 HIS A 18 PHE 0.017 0.002 PHE Y 23 TYR 0.017 0.002 TYR A 16 ARG 0.008 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 856) hydrogen bonds : angle 3.71617 ( 2565) covalent geometry : bond 0.00331 ( 9385) covalent geometry : angle 0.62641 (12686) *********************** 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 349 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 1.424 Fit side-chains REVERT: A 17 GLN cc_start: 0.9266 (mt0) cc_final: 0.8810 (mp10) REVERT: A 47 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8298 (tt0) REVERT: A 58 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8978 (mt-10) REVERT: A 60 GLN cc_start: 0.9287 (tt0) cc_final: 0.8865 (tm-30) REVERT: A 64 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7972 (pp20) REVERT: A 86 HIS cc_start: 0.8224 (t70) cc_final: 0.7619 (t70) REVERT: A 92 GLN cc_start: 0.8766 (tp40) cc_final: 0.8410 (tm-30) REVERT: A 94 GLU cc_start: 0.9139 (tp30) cc_final: 0.8654 (tp30) REVERT: A 96 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8398 (pt0) REVERT: A 105 GLU cc_start: 0.8897 (mp0) cc_final: 0.8616 (mp0) REVERT: A 109 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8886 (mt-10) REVERT: A 162 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9090 (p) REVERT: A 223 ASP cc_start: 0.8992 (m-30) cc_final: 0.8694 (m-30) REVERT: B 47 GLU cc_start: 0.9192 (tp30) cc_final: 0.8916 (tp30) REVERT: B 52 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8741 (ttpp) REVERT: B 64 GLU cc_start: 0.8832 (pm20) cc_final: 0.8478 (pm20) REVERT: B 66 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8582 (mmp80) REVERT: B 86 HIS cc_start: 0.8756 (t70) cc_final: 0.8388 (t70) REVERT: B 116 GLU cc_start: 0.9196 (tp30) cc_final: 0.8940 (tp30) REVERT: B 200 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.8416 (mtm180) REVERT: B 223 ASP cc_start: 0.9368 (t70) cc_final: 0.9102 (t0) REVERT: C 18 HIS cc_start: 0.9174 (t70) cc_final: 0.8532 (t-90) REVERT: C 47 GLU cc_start: 0.8886 (tp30) cc_final: 0.8489 (tt0) REVERT: C 64 GLU cc_start: 0.9048 (tp30) cc_final: 0.8259 (tp30) REVERT: C 66 ARG cc_start: 0.9080 (mtp85) cc_final: 0.8788 (mtp85) REVERT: C 72 ASN cc_start: 0.8523 (p0) cc_final: 0.8201 (p0) REVERT: C 93 ASN cc_start: 0.8974 (t0) cc_final: 0.8649 (t0) REVERT: C 94 GLU cc_start: 0.8972 (tp30) cc_final: 0.8218 (tp30) REVERT: C 103 ASP cc_start: 0.8910 (t0) cc_final: 0.8564 (t0) REVERT: C 105 GLU cc_start: 0.8587 (tp30) cc_final: 0.8335 (tp30) REVERT: C 114 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7581 (ttt90) REVERT: C 116 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 161 GLN cc_start: 0.9450 (mt0) cc_final: 0.8873 (mp10) REVERT: C 176 GLU cc_start: 0.9226 (tt0) cc_final: 0.8979 (tt0) REVERT: C 227 GLU cc_start: 0.9380 (tp30) cc_final: 0.8913 (tp30) REVERT: D 13 TRP cc_start: 0.9335 (t-100) cc_final: 0.9128 (t-100) REVERT: D 15 MET cc_start: 0.9342 (mpp) cc_final: 0.8547 (mpp) REVERT: D 18 HIS cc_start: 0.9172 (t70) cc_final: 0.8711 (t70) REVERT: D 50 ASN cc_start: 0.9067 (m-40) cc_final: 0.8779 (m-40) REVERT: D 223 ASP cc_start: 0.9227 (t0) cc_final: 0.8921 (m-30) REVERT: E 13 TRP cc_start: 0.9114 (t-100) cc_final: 0.8693 (t-100) REVERT: E 47 GLU cc_start: 0.9015 (tp30) cc_final: 0.8801 (tp30) REVERT: E 58 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8878 (mt-10) REVERT: E 86 HIS cc_start: 0.8357 (t70) cc_final: 0.8045 (t-90) REVERT: E 94 GLU cc_start: 0.9137 (tp30) cc_final: 0.8560 (tp30) REVERT: E 109 GLU cc_start: 0.9036 (tp30) cc_final: 0.8662 (tp30) REVERT: E 116 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 227 GLU cc_start: 0.9305 (tp30) cc_final: 0.9042 (tp30) REVERT: Z 19 ASN cc_start: 0.9326 (t0) cc_final: 0.9058 (t160) outliers start: 33 outliers final: 7 residues processed: 326 average time/residue: 1.6040 time to fit residues: 564.3731 Evaluate side-chains 308 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 299 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 34 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 50 ASN C 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.056093 restraints weight = 21141.967| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.20 r_work: 0.2680 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2936 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 : 0.591 10.667 12686 Z= 0.305 Chirality : 0.040 0.244 1496 Planarity : 0.003 0.028 1618 Dihedral : 6.525 129.095 1367 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 4.43 % Allowed : 17.51 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.23), residues: 1193 helix: 3.13 (0.15), residues: 1044 sheet: None (None), residues: 0 loop : -0.30 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 PHE 0.025 0.002 PHE C 156 TYR 0.020 0.002 TYR A 16 ARG 0.006 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 856) hydrogen bonds : angle 3.57431 ( 2565) covalent geometry : bond 0.00348 ( 9385) covalent geometry : angle 0.59099 (12686) *********************** 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 356 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 314 time to evaluate : 1.081 Fit side-chains REVERT: A 17 GLN cc_start: 0.9119 (mt0) cc_final: 0.8821 (mt0) REVERT: A 18 HIS cc_start: 0.8465 (p90) cc_final: 0.8111 (p-80) REVERT: A 47 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8527 (tt0) REVERT: A 58 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9124 (mt-10) REVERT: A 60 GLN cc_start: 0.9273 (tt0) cc_final: 0.8897 (tm-30) REVERT: A 86 HIS cc_start: 0.8386 (t70) cc_final: 0.7749 (t70) REVERT: A 92 GLN cc_start: 0.9016 (tp40) cc_final: 0.8412 (tm-30) REVERT: A 94 GLU cc_start: 0.9330 (tp30) cc_final: 0.8867 (tp30) REVERT: A 96 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8435 (mt-10) REVERT: A 103 ASP cc_start: 0.8837 (t0) cc_final: 0.8576 (t0) REVERT: A 105 GLU cc_start: 0.8902 (mp0) cc_final: 0.8699 (mp0) REVERT: A 109 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8977 (mt-10) REVERT: A 162 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9175 (p) REVERT: A 223 ASP cc_start: 0.9021 (m-30) cc_final: 0.8743 (m-30) REVERT: B 24 LYS cc_start: 0.8636 (mttp) cc_final: 0.8389 (mttm) REVERT: B 47 GLU cc_start: 0.9200 (tp30) cc_final: 0.8578 (tp30) REVERT: B 52 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8888 (ttpp) REVERT: B 58 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8938 (mm-30) REVERT: B 64 GLU cc_start: 0.8832 (pm20) cc_final: 0.8424 (pm20) REVERT: B 66 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8621 (mmp80) REVERT: B 86 HIS cc_start: 0.8779 (t70) cc_final: 0.8489 (t70) REVERT: B 93 ASN cc_start: 0.9185 (t0) cc_final: 0.8769 (t0) REVERT: B 116 GLU cc_start: 0.9185 (tp30) cc_final: 0.8961 (tp30) REVERT: B 162 THR cc_start: 0.9034 (t) cc_final: 0.8696 (p) REVERT: B 200 ARG cc_start: 0.8858 (tpp-160) cc_final: 0.8486 (ttm170) REVERT: B 223 ASP cc_start: 0.9344 (t70) cc_final: 0.9052 (t0) REVERT: C 18 HIS cc_start: 0.9125 (t70) cc_final: 0.8429 (t-90) REVERT: C 47 GLU cc_start: 0.9035 (tp30) cc_final: 0.8549 (tt0) REVERT: C 64 GLU cc_start: 0.9057 (tp30) cc_final: 0.8261 (tp30) REVERT: C 66 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8677 (mtp85) REVERT: C 81 LYS cc_start: 0.9255 (pmtt) cc_final: 0.8914 (pptt) REVERT: C 93 ASN cc_start: 0.9209 (t0) cc_final: 0.8867 (t0) REVERT: C 94 GLU cc_start: 0.9125 (tp30) cc_final: 0.8305 (tp30) REVERT: C 103 ASP cc_start: 0.9031 (t0) cc_final: 0.8742 (t0) REVERT: C 105 GLU cc_start: 0.8741 (tp30) cc_final: 0.8377 (tp30) REVERT: C 114 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7659 (ttt90) REVERT: C 116 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 161 GLN cc_start: 0.9451 (mt0) cc_final: 0.8898 (mp10) REVERT: C 176 GLU cc_start: 0.9268 (tt0) cc_final: 0.9044 (tt0) REVERT: C 223 ASP cc_start: 0.9134 (m-30) cc_final: 0.8916 (m-30) REVERT: C 227 GLU cc_start: 0.9406 (tp30) cc_final: 0.8927 (tp30) REVERT: D 13 TRP cc_start: 0.9335 (t-100) cc_final: 0.9122 (t-100) REVERT: D 15 MET cc_start: 0.9399 (mpp) cc_final: 0.8597 (mpp) REVERT: D 18 HIS cc_start: 0.9135 (t70) cc_final: 0.8683 (t70) REVERT: D 50 ASN cc_start: 0.9211 (m-40) cc_final: 0.8874 (m-40) REVERT: D 109 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8781 (mm-30) REVERT: D 223 ASP cc_start: 0.9206 (t0) cc_final: 0.8958 (t0) REVERT: E 13 TRP cc_start: 0.9125 (t-100) cc_final: 0.8657 (t-100) REVERT: E 58 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8913 (mt-10) REVERT: E 86 HIS cc_start: 0.8605 (t70) cc_final: 0.8342 (t-90) REVERT: E 94 GLU cc_start: 0.9254 (tp30) cc_final: 0.8811 (tp30) REVERT: E 223 ASP cc_start: 0.9108 (m-30) cc_final: 0.8666 (m-30) REVERT: E 227 GLU cc_start: 0.9336 (tp30) cc_final: 0.9064 (tp30) outliers start: 42 outliers final: 13 residues processed: 329 average time/residue: 1.0653 time to fit residues: 375.9273 Evaluate side-chains 319 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 304 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 114 ARG Chi-restraints excluded: chain C residue 186 VAL 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 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 69 ASN E 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056591 restraints weight = 21075.458| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.25 r_work: 0.2689 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 0.046 9385 Z= 0.144 Angle : 0.576 9.665 12686 Z= 0.297 Chirality : 0.039 0.265 1496 Planarity : 0.003 0.038 1618 Dihedral : 6.308 124.291 1367 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.69 % Allowed : 18.46 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.23), residues: 1193 helix: 3.25 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.37 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.002 0.001 HIS B 18 PHE 0.015 0.001 PHE D 48 TYR 0.020 0.002 TYR A 16 ARG 0.009 0.001 ARG E 118 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 856) hydrogen bonds : angle 3.44847 ( 2565) covalent geometry : bond 0.00325 ( 9385) covalent geometry : angle 0.57614 (12686) *********************** 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 350 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 315 time to evaluate : 0.982 Fit side-chains REVERT: A 17 GLN cc_start: 0.9163 (mt0) cc_final: 0.8868 (mp10) REVERT: A 18 HIS cc_start: 0.8580 (p90) cc_final: 0.8197 (p-80) REVERT: A 47 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8348 (tt0) REVERT: A 58 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9078 (mt-10) REVERT: A 60 GLN cc_start: 0.9291 (tt0) cc_final: 0.8901 (tm-30) REVERT: A 64 GLU cc_start: 0.8500 (pp20) cc_final: 0.8247 (pp20) REVERT: A 86 HIS cc_start: 0.8238 (t70) cc_final: 0.7592 (t70) REVERT: A 89 ASN cc_start: 0.8974 (m-40) cc_final: 0.8576 (m110) REVERT: A 92 GLN cc_start: 0.8744 (tp40) cc_final: 0.8158 (tm-30) REVERT: A 94 GLU cc_start: 0.9294 (tp30) cc_final: 0.8706 (tp30) REVERT: A 96 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 103 ASP cc_start: 0.8776 (t0) cc_final: 0.8397 (t0) REVERT: A 109 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8881 (mt-10) REVERT: A 223 ASP cc_start: 0.9040 (m-30) cc_final: 0.8723 (m-30) REVERT: B 47 GLU cc_start: 0.9194 (tp30) cc_final: 0.8615 (tm-30) REVERT: B 52 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8730 (ttpp) REVERT: B 64 GLU cc_start: 0.8711 (pm20) cc_final: 0.8401 (pm20) REVERT: B 66 ARG cc_start: 0.8979 (mmm-85) cc_final: 0.8569 (mmp80) REVERT: B 86 HIS cc_start: 0.8786 (t70) cc_final: 0.8346 (t70) REVERT: B 90 GLU cc_start: 0.8671 (tp30) cc_final: 0.8421 (mm-30) REVERT: B 93 ASN cc_start: 0.8972 (t0) cc_final: 0.8624 (t0) REVERT: B 105 GLU cc_start: 0.8850 (mp0) cc_final: 0.8486 (pm20) REVERT: B 116 GLU cc_start: 0.9108 (tp30) cc_final: 0.8861 (tp30) REVERT: B 166 ASN cc_start: 0.8441 (t0) cc_final: 0.8128 (t0) REVERT: B 200 ARG cc_start: 0.8787 (tpp-160) cc_final: 0.8267 (ttp-170) REVERT: B 223 ASP cc_start: 0.9383 (t70) cc_final: 0.9097 (t0) REVERT: C 18 HIS cc_start: 0.9136 (t70) cc_final: 0.8428 (t-90) REVERT: C 47 GLU cc_start: 0.8936 (tp30) cc_final: 0.8413 (tt0) REVERT: C 64 GLU cc_start: 0.9085 (tp30) cc_final: 0.8329 (tp30) REVERT: C 66 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8701 (mtp85) REVERT: C 81 LYS cc_start: 0.9258 (pmtt) cc_final: 0.9009 (pptt) REVERT: C 93 ASN cc_start: 0.8979 (t0) cc_final: 0.8661 (t0) REVERT: C 94 GLU cc_start: 0.9019 (tp30) cc_final: 0.8230 (tp30) REVERT: C 99 GLU cc_start: 0.8653 (pm20) cc_final: 0.8396 (pm20) REVERT: C 103 ASP cc_start: 0.8941 (t0) cc_final: 0.8541 (t0) REVERT: C 105 GLU cc_start: 0.8655 (tp30) cc_final: 0.8276 (tp30) REVERT: C 114 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7420 (ttt90) REVERT: C 116 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8263 (tm-30) REVERT: C 176 GLU cc_start: 0.9155 (tt0) cc_final: 0.8945 (tt0) REVERT: C 227 GLU cc_start: 0.9401 (tp30) cc_final: 0.8907 (tp30) REVERT: D 15 MET cc_start: 0.9257 (mpp) cc_final: 0.8499 (mpp) REVERT: D 18 HIS cc_start: 0.9193 (t70) cc_final: 0.8690 (t70) REVERT: D 50 ASN cc_start: 0.9060 (m-40) cc_final: 0.8745 (m-40) REVERT: D 109 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8727 (mm-30) REVERT: D 223 ASP cc_start: 0.9202 (t0) cc_final: 0.8981 (t0) REVERT: E 13 TRP cc_start: 0.9097 (t-100) cc_final: 0.8606 (t-100) REVERT: E 58 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8911 (mt-10) REVERT: E 86 HIS cc_start: 0.8424 (t70) cc_final: 0.8202 (t-90) REVERT: E 94 GLU cc_start: 0.9274 (tp30) cc_final: 0.8839 (tp30) REVERT: E 109 GLU cc_start: 0.9011 (tp30) cc_final: 0.8535 (tp30) REVERT: E 116 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8715 (tm-30) REVERT: E 223 ASP cc_start: 0.9083 (m-30) cc_final: 0.8637 (m-30) REVERT: E 227 GLU cc_start: 0.9337 (tp30) cc_final: 0.9065 (tp30) outliers start: 35 outliers final: 13 residues processed: 327 average time/residue: 1.1042 time to fit residues: 386.8288 Evaluate side-chains 317 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 303 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 LYS 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 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 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 1 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.073932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056977 restraints weight = 20895.980| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.17 r_work: 0.2713 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9385 Z= 0.146 Angle : 0.586 9.064 12686 Z= 0.302 Chirality : 0.039 0.262 1496 Planarity : 0.003 0.032 1618 Dihedral : 6.202 120.399 1367 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.59 % Allowed : 19.73 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.24), residues: 1193 helix: 3.30 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.39 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 13 HIS 0.002 0.000 HIS B 18 PHE 0.022 0.001 PHE C 156 TYR 0.021 0.002 TYR A 16 ARG 0.008 0.001 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 856) hydrogen bonds : angle 3.41250 ( 2565) covalent geometry : bond 0.00330 ( 9385) covalent geometry : angle 0.58617 (12686) *********************** 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: 34 poor density : 316 time to evaluate : 1.044 Fit side-chains REVERT: A 17 GLN cc_start: 0.9105 (mt0) cc_final: 0.8832 (mp10) REVERT: A 18 HIS cc_start: 0.8430 (p90) cc_final: 0.8070 (p-80) REVERT: A 47 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8509 (tt0) REVERT: A 60 GLN cc_start: 0.9287 (tt0) cc_final: 0.8918 (tm-30) REVERT: A 64 GLU cc_start: 0.8592 (pp20) cc_final: 0.8283 (pp20) REVERT: A 86 HIS cc_start: 0.8394 (t70) cc_final: 0.7822 (t70) REVERT: A 89 ASN cc_start: 0.9110 (m-40) cc_final: 0.8710 (m110) REVERT: A 92 GLN cc_start: 0.8944 (tp40) cc_final: 0.8263 (tm-30) REVERT: A 94 GLU cc_start: 0.9348 (tp30) cc_final: 0.8800 (tp30) REVERT: A 96 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8410 (mt-10) REVERT: A 109 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8964 (mt-10) REVERT: A 125 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8946 (tm-30) REVERT: A 223 ASP cc_start: 0.9024 (m-30) cc_final: 0.8726 (m-30) REVERT: B 24 LYS cc_start: 0.8567 (mttp) cc_final: 0.8342 (mttm) REVERT: B 47 GLU cc_start: 0.9202 (tp30) cc_final: 0.8680 (tm-30) REVERT: B 52 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8924 (ttpp) REVERT: B 64 GLU cc_start: 0.8771 (pm20) cc_final: 0.8411 (pm20) REVERT: B 66 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8657 (mmp80) REVERT: B 81 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8985 (mmmm) REVERT: B 86 HIS cc_start: 0.8820 (t70) cc_final: 0.8381 (t70) REVERT: B 90 GLU cc_start: 0.8770 (tp30) cc_final: 0.8505 (mm-30) REVERT: B 93 ASN cc_start: 0.9223 (t0) cc_final: 0.8843 (t0) REVERT: B 103 ASP cc_start: 0.8777 (t0) cc_final: 0.8361 (t0) REVERT: B 105 GLU cc_start: 0.8930 (mp0) cc_final: 0.8578 (pm20) REVERT: B 109 GLU cc_start: 0.9107 (pt0) cc_final: 0.8893 (tp30) REVERT: B 116 GLU cc_start: 0.9143 (tp30) cc_final: 0.8916 (tp30) REVERT: B 132 TYR cc_start: 0.8981 (t80) cc_final: 0.8721 (t80) REVERT: B 162 THR cc_start: 0.8882 (t) cc_final: 0.8546 (p) REVERT: B 166 ASN cc_start: 0.8622 (t0) cc_final: 0.8280 (t0) REVERT: B 200 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8413 (ttp-170) REVERT: B 223 ASP cc_start: 0.9351 (t70) cc_final: 0.9038 (t0) REVERT: C 18 HIS cc_start: 0.9065 (t70) cc_final: 0.8305 (t-90) REVERT: C 47 GLU cc_start: 0.9041 (tp30) cc_final: 0.8551 (tt0) REVERT: C 58 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8739 (mm-30) REVERT: C 64 GLU cc_start: 0.9069 (tp30) cc_final: 0.8383 (tp30) REVERT: C 66 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8749 (mtp85) REVERT: C 72 ASN cc_start: 0.8352 (p0) cc_final: 0.8098 (p0) REVERT: C 81 LYS cc_start: 0.9209 (pmtt) cc_final: 0.9008 (pptt) REVERT: C 93 ASN cc_start: 0.9229 (t0) cc_final: 0.8886 (t0) REVERT: C 94 GLU cc_start: 0.9109 (tp30) cc_final: 0.8361 (tp30) REVERT: C 103 ASP cc_start: 0.9071 (t0) cc_final: 0.8585 (t0) REVERT: C 114 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7685 (ttt90) REVERT: C 116 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 176 GLU cc_start: 0.9223 (tt0) cc_final: 0.8980 (tt0) REVERT: C 227 GLU cc_start: 0.9392 (tp30) cc_final: 0.8876 (tp30) REVERT: D 15 MET cc_start: 0.9350 (mpp) cc_final: 0.8566 (mpp) REVERT: D 18 HIS cc_start: 0.9094 (t70) cc_final: 0.8545 (t70) REVERT: D 50 ASN cc_start: 0.9198 (m-40) cc_final: 0.8867 (m-40) REVERT: D 223 ASP cc_start: 0.9179 (t0) cc_final: 0.8945 (t0) REVERT: E 13 TRP cc_start: 0.9050 (t-100) cc_final: 0.8587 (t-100) REVERT: E 58 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8897 (mt-10) REVERT: E 86 HIS cc_start: 0.8561 (t70) cc_final: 0.8225 (t-170) REVERT: E 94 GLU cc_start: 0.9337 (tp30) cc_final: 0.8964 (tp30) REVERT: E 109 GLU cc_start: 0.9013 (tp30) cc_final: 0.8691 (tp30) REVERT: E 153 MET cc_start: 0.9079 (ttm) cc_final: 0.8824 (ttm) REVERT: E 223 ASP cc_start: 0.9096 (m-30) cc_final: 0.8644 (m-30) REVERT: E 227 GLU cc_start: 0.9339 (tp30) cc_final: 0.9053 (tp30) REVERT: Z 35 MET cc_start: 0.8755 (tpp) cc_final: 0.7942 (mpp) outliers start: 34 outliers final: 16 residues processed: 329 average time/residue: 1.1369 time to fit residues: 400.5803 Evaluate side-chains 320 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 303 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 77 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 85 LEU 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 D residue 179 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 51 GLN A 72 ASN B 50 ASN B 161 GLN C 154 ASN D 69 ASN E 50 ASN Z 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056027 restraints weight = 21118.189| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.23 r_work: 0.2684 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9385 Z= 0.163 Angle : 0.608 8.877 12686 Z= 0.312 Chirality : 0.040 0.257 1496 Planarity : 0.003 0.038 1618 Dihedral : 6.180 118.005 1367 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.38 % Allowed : 21.94 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.24), residues: 1193 helix: 3.28 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.33 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 13 HIS 0.002 0.000 HIS D 18 PHE 0.026 0.001 PHE Z 34 TYR 0.022 0.002 TYR A 16 ARG 0.011 0.001 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 856) hydrogen bonds : angle 3.46644 ( 2565) covalent geometry : bond 0.00376 ( 9385) covalent geometry : angle 0.60826 (12686) *********************** 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 341 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 309 time to evaluate : 1.056 Fit side-chains REVERT: A 17 GLN cc_start: 0.9149 (mt0) cc_final: 0.8852 (mt0) REVERT: A 18 HIS cc_start: 0.8632 (p90) cc_final: 0.8283 (p-80) REVERT: A 47 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8329 (tt0) REVERT: A 60 GLN cc_start: 0.9293 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 64 GLU cc_start: 0.8608 (pp20) cc_final: 0.8261 (pp20) REVERT: A 86 HIS cc_start: 0.8220 (t70) cc_final: 0.7525 (t70) REVERT: A 89 ASN cc_start: 0.8972 (m-40) cc_final: 0.8583 (m110) REVERT: A 92 GLN cc_start: 0.8714 (tp40) cc_final: 0.8112 (tm-30) REVERT: A 94 GLU cc_start: 0.9279 (tp30) cc_final: 0.8692 (tp30) REVERT: A 96 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 109 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8873 (mt-10) REVERT: A 125 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 223 ASP cc_start: 0.9041 (m-30) cc_final: 0.8713 (m-30) REVERT: B 47 GLU cc_start: 0.9173 (tp30) cc_final: 0.8588 (tm-30) REVERT: B 52 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8749 (ttpp) REVERT: B 64 GLU cc_start: 0.8708 (pm20) cc_final: 0.8457 (pm20) REVERT: B 66 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8633 (mmp80) REVERT: B 81 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8969 (mmmm) REVERT: B 86 HIS cc_start: 0.8764 (t70) cc_final: 0.8305 (t70) REVERT: B 90 GLU cc_start: 0.8646 (tp30) cc_final: 0.8392 (mm-30) REVERT: B 93 ASN cc_start: 0.8960 (t0) cc_final: 0.8605 (t0) REVERT: B 105 GLU cc_start: 0.8867 (mp0) cc_final: 0.8497 (pm20) REVERT: B 116 GLU cc_start: 0.9100 (tp30) cc_final: 0.8848 (tp30) REVERT: B 166 ASN cc_start: 0.8538 (t0) cc_final: 0.8272 (m-40) REVERT: B 200 ARG cc_start: 0.8833 (tpp-160) cc_final: 0.8389 (ttm170) REVERT: B 223 ASP cc_start: 0.9369 (t70) cc_final: 0.9073 (t0) REVERT: C 10 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8371 (tp) REVERT: C 18 HIS cc_start: 0.9071 (t70) cc_final: 0.8326 (t-90) REVERT: C 47 GLU cc_start: 0.8965 (tp30) cc_final: 0.8437 (tt0) REVERT: C 52 LYS cc_start: 0.8936 (tptm) cc_final: 0.8706 (tptt) REVERT: C 58 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8742 (mm-30) REVERT: C 64 GLU cc_start: 0.9080 (tp30) cc_final: 0.8338 (tp30) REVERT: C 66 ARG cc_start: 0.9033 (mtp85) cc_final: 0.8655 (mtp85) REVERT: C 72 ASN cc_start: 0.8172 (p0) cc_final: 0.7936 (p0) REVERT: C 93 ASN cc_start: 0.8976 (t0) cc_final: 0.8672 (t0) REVERT: C 94 GLU cc_start: 0.9065 (tp30) cc_final: 0.8324 (tp30) REVERT: C 103 ASP cc_start: 0.8616 (t0) cc_final: 0.7606 (t0) REVERT: C 114 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7473 (ttt90) REVERT: C 116 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 176 GLU cc_start: 0.9139 (tt0) cc_final: 0.8897 (tt0) REVERT: C 227 GLU cc_start: 0.9421 (tp30) cc_final: 0.8928 (tp30) REVERT: D 15 MET cc_start: 0.9224 (mpp) cc_final: 0.8481 (mpp) REVERT: D 18 HIS cc_start: 0.9075 (t70) cc_final: 0.8490 (t70) REVERT: D 50 ASN cc_start: 0.9080 (m-40) cc_final: 0.8787 (m-40) REVERT: D 109 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8748 (mm-30) REVERT: D 223 ASP cc_start: 0.9201 (t0) cc_final: 0.8986 (t0) REVERT: E 13 TRP cc_start: 0.9036 (t-100) cc_final: 0.8550 (t-100) REVERT: E 24 LYS cc_start: 0.8607 (mttp) cc_final: 0.8329 (mttm) REVERT: E 58 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8901 (mt-10) REVERT: E 86 HIS cc_start: 0.8420 (t70) cc_final: 0.8143 (t-90) REVERT: E 94 GLU cc_start: 0.9357 (tp30) cc_final: 0.8889 (tp30) REVERT: E 109 GLU cc_start: 0.9016 (tp30) cc_final: 0.8586 (tp30) REVERT: E 116 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8738 (tm-30) REVERT: E 223 ASP cc_start: 0.9070 (m-30) cc_final: 0.8618 (m-30) REVERT: E 227 GLU cc_start: 0.9337 (tp30) cc_final: 0.9058 (tp30) outliers start: 32 outliers final: 20 residues processed: 323 average time/residue: 1.1839 time to fit residues: 410.9627 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 : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 LYS 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 B residue 202 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.073420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056894 restraints weight = 21349.419| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.17 r_work: 0.2701 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9385 Z= 0.150 Angle : 0.647 16.605 12686 Z= 0.322 Chirality : 0.041 0.289 1496 Planarity : 0.003 0.044 1618 Dihedral : 6.147 116.547 1367 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.16 % Allowed : 23.95 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.24), residues: 1193 helix: 3.25 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.37 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 13 HIS 0.001 0.000 HIS B 18 PHE 0.016 0.001 PHE D 48 TYR 0.023 0.002 TYR A 16 ARG 0.010 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 856) hydrogen bonds : angle 3.47014 ( 2565) covalent geometry : bond 0.00342 ( 9385) covalent geometry : angle 0.64687 (12686) *********************** 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 342 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 1.049 Fit side-chains REVERT: A 17 GLN cc_start: 0.9136 (mt0) cc_final: 0.8829 (mt0) REVERT: A 18 HIS cc_start: 0.8642 (p90) cc_final: 0.8284 (p-80) REVERT: A 47 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8361 (tt0) REVERT: A 60 GLN cc_start: 0.9281 (tt0) cc_final: 0.8911 (tm-30) REVERT: A 64 GLU cc_start: 0.8618 (pp20) cc_final: 0.8247 (pp20) REVERT: A 86 HIS cc_start: 0.8186 (t70) cc_final: 0.7590 (t70) REVERT: A 89 ASN cc_start: 0.8985 (m-40) cc_final: 0.8590 (m110) REVERT: A 92 GLN cc_start: 0.8717 (tp40) cc_final: 0.8108 (tm-30) REVERT: A 94 GLU cc_start: 0.9268 (tp30) cc_final: 0.8712 (tp30) REVERT: A 96 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8401 (mt-10) REVERT: A 109 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8852 (mt-10) REVERT: A 125 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 223 ASP cc_start: 0.9038 (m-30) cc_final: 0.8706 (m-30) REVERT: B 47 GLU cc_start: 0.9174 (tp30) cc_final: 0.8608 (tm-30) REVERT: B 52 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8777 (ttpp) REVERT: B 64 GLU cc_start: 0.8711 (pm20) cc_final: 0.8455 (pm20) REVERT: B 66 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8642 (mmp80) REVERT: B 81 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9046 (mmmm) REVERT: B 86 HIS cc_start: 0.8765 (t70) cc_final: 0.8357 (t70) REVERT: B 90 GLU cc_start: 0.8618 (tp30) cc_final: 0.8356 (mm-30) REVERT: B 93 ASN cc_start: 0.9005 (t0) cc_final: 0.8647 (t0) REVERT: B 103 ASP cc_start: 0.8719 (t0) cc_final: 0.8224 (t0) REVERT: B 105 GLU cc_start: 0.8886 (mp0) cc_final: 0.8522 (pm20) REVERT: B 116 GLU cc_start: 0.9092 (tp30) cc_final: 0.8844 (tp30) REVERT: B 162 THR cc_start: 0.8554 (t) cc_final: 0.8213 (p) REVERT: B 166 ASN cc_start: 0.8578 (t0) cc_final: 0.8301 (m-40) REVERT: B 200 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8375 (ttm170) REVERT: B 223 ASP cc_start: 0.9326 (t70) cc_final: 0.9051 (t0) REVERT: C 10 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8458 (tp) REVERT: C 18 HIS cc_start: 0.9066 (t70) cc_final: 0.8300 (t-90) REVERT: C 47 GLU cc_start: 0.8973 (tp30) cc_final: 0.8455 (tt0) REVERT: C 58 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8708 (mm-30) REVERT: C 64 GLU cc_start: 0.9076 (tp30) cc_final: 0.8349 (tp30) REVERT: C 66 ARG cc_start: 0.9027 (mtp85) cc_final: 0.8652 (mtp85) REVERT: C 72 ASN cc_start: 0.8195 (p0) cc_final: 0.7948 (p0) REVERT: C 93 ASN cc_start: 0.8957 (t0) cc_final: 0.8645 (t0) REVERT: C 94 GLU cc_start: 0.9034 (tp30) cc_final: 0.8598 (tp30) REVERT: C 103 ASP cc_start: 0.8737 (t0) cc_final: 0.8123 (t0) REVERT: C 116 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8376 (tm-30) REVERT: C 176 GLU cc_start: 0.9132 (tt0) cc_final: 0.8875 (tt0) REVERT: C 227 GLU cc_start: 0.9418 (tp30) cc_final: 0.8925 (tp30) REVERT: D 15 MET cc_start: 0.9225 (mpp) cc_final: 0.8495 (mpp) REVERT: D 16 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8659 (t80) REVERT: D 18 HIS cc_start: 0.9047 (t70) cc_final: 0.8436 (t70) REVERT: D 50 ASN cc_start: 0.9104 (m-40) cc_final: 0.8809 (m-40) REVERT: D 109 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8714 (mm-30) REVERT: D 223 ASP cc_start: 0.9176 (t0) cc_final: 0.8962 (t0) REVERT: E 13 TRP cc_start: 0.9030 (t-100) cc_final: 0.8538 (t-100) REVERT: E 58 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8875 (mt-10) REVERT: E 86 HIS cc_start: 0.8428 (t70) cc_final: 0.7993 (t-170) REVERT: E 94 GLU cc_start: 0.9357 (tp30) cc_final: 0.8907 (tp30) REVERT: E 109 GLU cc_start: 0.9028 (tp30) cc_final: 0.8598 (tp30) REVERT: E 116 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8591 (tp30) REVERT: E 223 ASP cc_start: 0.9061 (m-30) cc_final: 0.8606 (m-30) REVERT: E 227 GLU cc_start: 0.9341 (tp30) cc_final: 0.9056 (tp30) outliers start: 30 outliers final: 21 residues processed: 322 average time/residue: 1.4879 time to fit residues: 520.3855 Evaluate side-chains 326 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 A residue 164 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 16 TYR 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 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 51 GLN B 50 ASN D 69 ASN E 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056363 restraints weight = 21262.738| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.21 r_work: 0.2709 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9385 Z= 0.167 Angle : 0.658 12.102 12686 Z= 0.332 Chirality : 0.042 0.309 1496 Planarity : 0.003 0.047 1618 Dihedral : 6.156 115.172 1367 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.48 % Allowed : 24.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.24), residues: 1193 helix: 3.25 (0.15), residues: 1047 sheet: None (None), residues: 0 loop : -0.36 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 13 HIS 0.002 0.000 HIS B 18 PHE 0.017 0.001 PHE D 48 TYR 0.024 0.002 TYR A 16 ARG 0.011 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 856) hydrogen bonds : angle 3.49794 ( 2565) covalent geometry : bond 0.00388 ( 9385) covalent geometry : angle 0.65765 (12686) *********************** 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 341 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 0.816 Fit side-chains REVERT: A 17 GLN cc_start: 0.9089 (mt0) cc_final: 0.8812 (mt0) REVERT: A 18 HIS cc_start: 0.8617 (p90) cc_final: 0.8192 (p-80) REVERT: A 47 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8505 (tt0) REVERT: A 60 GLN cc_start: 0.9302 (tt0) cc_final: 0.8941 (tm-30) REVERT: A 64 GLU cc_start: 0.8691 (pp20) cc_final: 0.8329 (pp20) REVERT: A 86 HIS cc_start: 0.8386 (t70) cc_final: 0.7774 (t70) REVERT: A 89 ASN cc_start: 0.9130 (m-40) cc_final: 0.8734 (m110) REVERT: A 92 GLN cc_start: 0.8932 (tp40) cc_final: 0.8290 (tm-30) REVERT: A 94 GLU cc_start: 0.9349 (tp30) cc_final: 0.8774 (tp30) REVERT: A 96 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 109 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8931 (mt-10) REVERT: A 125 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 223 ASP cc_start: 0.9057 (m-30) cc_final: 0.8760 (m-30) REVERT: B 47 GLU cc_start: 0.9211 (tp30) cc_final: 0.8650 (tm-30) REVERT: B 52 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8949 (ttpp) REVERT: B 64 GLU cc_start: 0.8772 (pm20) cc_final: 0.8486 (pm20) REVERT: B 66 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8676 (mmp80) REVERT: B 81 LYS cc_start: 0.9274 (mmmm) cc_final: 0.9015 (mmmm) REVERT: B 86 HIS cc_start: 0.8833 (t70) cc_final: 0.8473 (t70) REVERT: B 93 ASN cc_start: 0.9193 (t0) cc_final: 0.8794 (t0) REVERT: B 105 GLU cc_start: 0.8965 (mp0) cc_final: 0.8554 (pm20) REVERT: B 162 THR cc_start: 0.8764 (t) cc_final: 0.8414 (p) REVERT: B 166 ASN cc_start: 0.8690 (t0) cc_final: 0.8424 (m110) REVERT: B 200 ARG cc_start: 0.8913 (tpp-160) cc_final: 0.8486 (ttm170) REVERT: B 223 ASP cc_start: 0.9325 (t70) cc_final: 0.9045 (t0) REVERT: C 10 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8421 (tp) REVERT: C 18 HIS cc_start: 0.9041 (t70) cc_final: 0.8324 (t-90) REVERT: C 47 GLU cc_start: 0.9036 (tp30) cc_final: 0.8541 (tt0) REVERT: C 52 LYS cc_start: 0.9195 (tptm) cc_final: 0.8958 (tptt) REVERT: C 58 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8857 (mm-30) REVERT: C 64 GLU cc_start: 0.9083 (tp30) cc_final: 0.8542 (tm-30) REVERT: C 66 ARG cc_start: 0.9061 (mtp85) cc_final: 0.8807 (mtp85) REVERT: C 72 ASN cc_start: 0.8333 (p0) cc_final: 0.8065 (p0) REVERT: C 93 ASN cc_start: 0.9147 (t0) cc_final: 0.8832 (t0) REVERT: C 94 GLU cc_start: 0.9148 (tp30) cc_final: 0.8558 (tp30) REVERT: C 103 ASP cc_start: 0.8784 (t0) cc_final: 0.8273 (t0) REVERT: C 109 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8841 (tp30) REVERT: C 116 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 176 GLU cc_start: 0.9188 (tt0) cc_final: 0.8957 (tt0) REVERT: C 227 GLU cc_start: 0.9417 (tp30) cc_final: 0.8919 (tp30) REVERT: D 15 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8636 (mpp) REVERT: D 18 HIS cc_start: 0.9003 (t70) cc_final: 0.8416 (t70) REVERT: D 50 ASN cc_start: 0.9213 (m-40) cc_final: 0.8895 (m-40) REVERT: D 109 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8800 (mm-30) REVERT: D 223 ASP cc_start: 0.9191 (t0) cc_final: 0.8960 (t0) REVERT: E 13 TRP cc_start: 0.9018 (t-100) cc_final: 0.8555 (t-100) REVERT: E 24 LYS cc_start: 0.8837 (mttp) cc_final: 0.8534 (mmtm) REVERT: E 58 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8905 (mt-10) REVERT: E 86 HIS cc_start: 0.8582 (t70) cc_final: 0.8169 (t-170) REVERT: E 94 GLU cc_start: 0.9433 (tp30) cc_final: 0.9013 (tp30) REVERT: E 109 GLU cc_start: 0.9021 (tp30) cc_final: 0.8581 (tp30) REVERT: E 116 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8700 (tp30) REVERT: E 223 ASP cc_start: 0.9100 (m-30) cc_final: 0.8652 (m-30) REVERT: E 227 GLU cc_start: 0.9346 (tp30) cc_final: 0.9059 (tp30) outliers start: 33 outliers final: 23 residues processed: 319 average time/residue: 1.0437 time to fit residues: 357.8930 Evaluate side-chains 325 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 B residue 202 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 81 LYS 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 186 VAL 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 Y residue 31 LEU Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 62 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.073219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056681 restraints weight = 20974.628| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.09 r_work: 0.2726 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9385 Z= 0.168 Angle : 0.688 13.924 12686 Z= 0.345 Chirality : 0.043 0.328 1496 Planarity : 0.003 0.053 1618 Dihedral : 6.166 114.450 1367 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.74 % Allowed : 25.84 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.24), residues: 1193 helix: 3.23 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 13 HIS 0.003 0.000 HIS B 18 PHE 0.020 0.001 PHE Z 34 TYR 0.022 0.002 TYR A 16 ARG 0.013 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 856) hydrogen bonds : angle 3.51211 ( 2565) covalent geometry : bond 0.00391 ( 9385) covalent geometry : angle 0.68799 (12686) *********************** 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 333 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 0.981 Fit side-chains REVERT: A 17 GLN cc_start: 0.9123 (mt0) cc_final: 0.8826 (mt0) REVERT: A 18 HIS cc_start: 0.8615 (p90) cc_final: 0.8216 (p-80) REVERT: A 47 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8545 (tt0) REVERT: A 60 GLN cc_start: 0.9310 (tt0) cc_final: 0.8947 (tm-30) REVERT: A 64 GLU cc_start: 0.8698 (pp20) cc_final: 0.8328 (pp20) REVERT: A 86 HIS cc_start: 0.8362 (t70) cc_final: 0.7769 (t70) REVERT: A 89 ASN cc_start: 0.9125 (m-40) cc_final: 0.8706 (m110) REVERT: A 92 GLN cc_start: 0.8926 (tp40) cc_final: 0.8281 (tm-30) REVERT: A 94 GLU cc_start: 0.9346 (tp30) cc_final: 0.8789 (tp30) REVERT: A 96 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 109 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8921 (mt-10) REVERT: A 125 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8876 (tm-30) REVERT: A 223 ASP cc_start: 0.9045 (m-30) cc_final: 0.8745 (m-30) REVERT: B 47 GLU cc_start: 0.9219 (tp30) cc_final: 0.8608 (tm-30) REVERT: B 52 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8960 (ttpp) REVERT: B 64 GLU cc_start: 0.8752 (pm20) cc_final: 0.8461 (pm20) REVERT: B 66 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8681 (mmp80) REVERT: B 81 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9034 (mmmm) REVERT: B 86 HIS cc_start: 0.8827 (t70) cc_final: 0.8518 (t70) REVERT: B 90 GLU cc_start: 0.8766 (tp30) cc_final: 0.8421 (tt0) REVERT: B 93 ASN cc_start: 0.9210 (t0) cc_final: 0.8817 (t0) REVERT: B 103 ASP cc_start: 0.8615 (t0) cc_final: 0.8281 (t0) REVERT: B 105 GLU cc_start: 0.8952 (mp0) cc_final: 0.8567 (pm20) REVERT: B 109 GLU cc_start: 0.9127 (pt0) cc_final: 0.8869 (tp30) REVERT: B 162 THR cc_start: 0.8741 (t) cc_final: 0.8396 (p) REVERT: B 166 ASN cc_start: 0.8707 (t0) cc_final: 0.8437 (m110) REVERT: B 200 ARG cc_start: 0.8917 (tpp-160) cc_final: 0.8346 (ttp-170) REVERT: B 223 ASP cc_start: 0.9314 (t70) cc_final: 0.9016 (t0) REVERT: C 10 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (tp) REVERT: C 15 MET cc_start: 0.8930 (mtp) cc_final: 0.8463 (mtp) REVERT: C 18 HIS cc_start: 0.9041 (t70) cc_final: 0.8336 (t-90) REVERT: C 47 GLU cc_start: 0.9049 (tp30) cc_final: 0.8553 (tt0) REVERT: C 52 LYS cc_start: 0.9198 (tptm) cc_final: 0.8958 (tptt) REVERT: C 58 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8891 (mm-30) REVERT: C 64 GLU cc_start: 0.9071 (tp30) cc_final: 0.8536 (tm-30) REVERT: C 66 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8798 (mtp85) REVERT: C 72 ASN cc_start: 0.8329 (p0) cc_final: 0.8065 (p0) REVERT: C 93 ASN cc_start: 0.9144 (t0) cc_final: 0.8813 (t0) REVERT: C 94 GLU cc_start: 0.9167 (tp30) cc_final: 0.8575 (tp30) REVERT: C 103 ASP cc_start: 0.8727 (t0) cc_final: 0.8266 (t0) REVERT: C 109 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8835 (tp30) REVERT: C 116 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 176 GLU cc_start: 0.9187 (tt0) cc_final: 0.8976 (tt0) REVERT: C 227 GLU cc_start: 0.9407 (tp30) cc_final: 0.8906 (tp30) REVERT: D 15 MET cc_start: 0.9307 (mpp) cc_final: 0.8621 (mpp) REVERT: D 18 HIS cc_start: 0.8995 (t70) cc_final: 0.8351 (t70) REVERT: D 50 ASN cc_start: 0.9213 (m-40) cc_final: 0.8900 (m110) REVERT: D 109 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8803 (mm-30) REVERT: D 223 ASP cc_start: 0.9185 (t0) cc_final: 0.8955 (t0) REVERT: E 13 TRP cc_start: 0.9027 (t-100) cc_final: 0.8550 (t-100) REVERT: E 24 LYS cc_start: 0.8832 (mttp) cc_final: 0.8556 (mttm) REVERT: E 58 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8898 (mt-10) REVERT: E 86 HIS cc_start: 0.8584 (t70) cc_final: 0.8177 (t-170) REVERT: E 94 GLU cc_start: 0.9424 (tp30) cc_final: 0.9018 (tp30) REVERT: E 109 GLU cc_start: 0.9021 (tp30) cc_final: 0.8684 (tp30) REVERT: E 174 ILE cc_start: 0.9414 (pt) cc_final: 0.9027 (pt) REVERT: E 223 ASP cc_start: 0.9097 (m-30) cc_final: 0.8646 (m-30) REVERT: E 227 GLU cc_start: 0.9345 (tp30) cc_final: 0.9054 (tp30) REVERT: Z 35 MET cc_start: 0.8523 (tpp) cc_final: 0.7859 (mpp) outliers start: 26 outliers final: 23 residues processed: 317 average time/residue: 1.0382 time to fit residues: 353.6394 Evaluate side-chains 329 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 ASP 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 B residue 202 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 81 LYS 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 E residue 32 LEU Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 51 GLN 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 = 0.3263 r_free = 0.3263 target = 0.074000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057009 restraints weight = 21102.512| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.19 r_work: 0.2724 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9385 Z= 0.156 Angle : 0.717 15.354 12686 Z= 0.353 Chirality : 0.044 0.333 1496 Planarity : 0.003 0.056 1618 Dihedral : 6.137 113.395 1367 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.64 % Allowed : 25.95 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.30 (0.24), residues: 1193 helix: 3.22 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.45 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 13 HIS 0.003 0.000 HIS B 18 PHE 0.016 0.001 PHE D 48 TYR 0.024 0.002 TYR A 16 ARG 0.014 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 856) hydrogen bonds : angle 3.52428 ( 2565) covalent geometry : bond 0.00361 ( 9385) covalent geometry : angle 0.71730 (12686) ********************** 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: 25 poor density : 304 time to evaluate : 0.924 Fit side-chains REVERT: A 17 GLN cc_start: 0.9117 (mt0) cc_final: 0.8803 (mt0) REVERT: A 18 HIS cc_start: 0.8600 (p90) cc_final: 0.8204 (p-80) REVERT: A 47 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8530 (tt0) REVERT: A 60 GLN cc_start: 0.9291 (tt0) cc_final: 0.8932 (tm-30) REVERT: A 64 GLU cc_start: 0.8699 (pp20) cc_final: 0.8324 (pp20) REVERT: A 86 HIS cc_start: 0.8352 (t70) cc_final: 0.7774 (t70) REVERT: A 89 ASN cc_start: 0.9125 (m-40) cc_final: 0.8715 (m110) REVERT: A 92 GLN cc_start: 0.8924 (tp40) cc_final: 0.8274 (tm-30) REVERT: A 94 GLU cc_start: 0.9332 (tp30) cc_final: 0.8771 (tp30) REVERT: A 96 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 109 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8914 (mt-10) REVERT: A 125 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8871 (tm-30) REVERT: A 223 ASP cc_start: 0.9040 (m-30) cc_final: 0.8739 (m-30) REVERT: B 47 GLU cc_start: 0.9220 (tp30) cc_final: 0.8650 (tm-30) REVERT: B 52 LYS cc_start: 0.9172 (ttpp) cc_final: 0.8955 (ttpp) REVERT: B 64 GLU cc_start: 0.8766 (pm20) cc_final: 0.8497 (pm20) REVERT: B 66 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8672 (mmp80) REVERT: B 81 LYS cc_start: 0.9279 (mmmm) cc_final: 0.9018 (mmmm) REVERT: B 86 HIS cc_start: 0.8832 (t70) cc_final: 0.8547 (t70) REVERT: B 90 GLU cc_start: 0.8725 (tp30) cc_final: 0.8469 (tt0) REVERT: B 93 ASN cc_start: 0.9185 (t0) cc_final: 0.8793 (t0) REVERT: B 103 ASP cc_start: 0.8734 (t0) cc_final: 0.8088 (t0) REVERT: B 105 GLU cc_start: 0.8934 (mp0) cc_final: 0.8560 (pm20) REVERT: B 109 GLU cc_start: 0.9131 (pt0) cc_final: 0.8862 (tp30) REVERT: B 162 THR cc_start: 0.8729 (t) cc_final: 0.8379 (p) REVERT: B 166 ASN cc_start: 0.8701 (t0) cc_final: 0.8435 (m110) REVERT: B 200 ARG cc_start: 0.8918 (tpp-160) cc_final: 0.8349 (ttp-170) REVERT: B 223 ASP cc_start: 0.9318 (t70) cc_final: 0.9019 (t0) REVERT: C 10 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 15 MET cc_start: 0.8923 (mtp) cc_final: 0.8463 (mtp) REVERT: C 18 HIS cc_start: 0.9031 (t70) cc_final: 0.8316 (t-90) REVERT: C 47 GLU cc_start: 0.9042 (tp30) cc_final: 0.8548 (tt0) REVERT: C 52 LYS cc_start: 0.9205 (tptm) cc_final: 0.8966 (tptt) REVERT: C 58 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8895 (mm-30) REVERT: C 64 GLU cc_start: 0.9061 (tp30) cc_final: 0.8553 (tm-30) REVERT: C 66 ARG cc_start: 0.9055 (mtp85) cc_final: 0.8805 (mtp85) REVERT: C 72 ASN cc_start: 0.8315 (p0) cc_final: 0.8052 (p0) REVERT: C 93 ASN cc_start: 0.9146 (t0) cc_final: 0.8809 (t0) REVERT: C 94 GLU cc_start: 0.9153 (tp30) cc_final: 0.8540 (tp30) REVERT: C 103 ASP cc_start: 0.8700 (t0) cc_final: 0.8263 (t0) REVERT: C 109 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8835 (tp30) REVERT: C 116 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 176 GLU cc_start: 0.9172 (tt0) cc_final: 0.8971 (tt0) REVERT: C 223 ASP cc_start: 0.9069 (m-30) cc_final: 0.8729 (m-30) REVERT: C 227 GLU cc_start: 0.9417 (tp30) cc_final: 0.8919 (tp30) REVERT: D 15 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8624 (mpp) REVERT: D 18 HIS cc_start: 0.9102 (t70) cc_final: 0.8532 (t70) REVERT: D 50 ASN cc_start: 0.9208 (m-40) cc_final: 0.8895 (m110) REVERT: D 109 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8798 (mm-30) REVERT: D 223 ASP cc_start: 0.9184 (t0) cc_final: 0.8953 (t0) REVERT: E 13 TRP cc_start: 0.9008 (t-100) cc_final: 0.8525 (t-100) REVERT: E 24 LYS cc_start: 0.8829 (mttp) cc_final: 0.8549 (mttm) REVERT: E 58 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8936 (mt-10) REVERT: E 86 HIS cc_start: 0.8565 (t70) cc_final: 0.8151 (t-170) REVERT: E 94 GLU cc_start: 0.9417 (tp30) cc_final: 0.9024 (tp30) REVERT: E 109 GLU cc_start: 0.9004 (tp30) cc_final: 0.8561 (tp30) REVERT: E 116 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8696 (tp30) REVERT: E 223 ASP cc_start: 0.9100 (m-30) cc_final: 0.8650 (m-30) REVERT: E 227 GLU cc_start: 0.9342 (tp30) cc_final: 0.9059 (tp30) REVERT: Y 34 PHE cc_start: 0.8297 (m-80) cc_final: 0.8064 (t80) outliers start: 25 outliers final: 22 residues processed: 311 average time/residue: 1.0022 time to fit residues: 335.6116 Evaluate side-chains 323 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 B residue 202 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 81 LYS 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 164 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 E 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057563 restraints weight = 21008.112| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.11 r_work: 0.2734 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9385 Z= 0.152 Angle : 0.694 15.103 12686 Z= 0.345 Chirality : 0.043 0.337 1496 Planarity : 0.003 0.055 1618 Dihedral : 6.116 112.328 1367 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.74 % Allowed : 26.05 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.24), residues: 1193 helix: 3.25 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.44 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 13 HIS 0.002 0.000 HIS B 18 PHE 0.016 0.001 PHE D 48 TYR 0.025 0.002 TYR A 16 ARG 0.013 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 856) hydrogen bonds : angle 3.50212 ( 2565) covalent geometry : bond 0.00350 ( 9385) covalent geometry : angle 0.69429 (12686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8543.95 seconds wall clock time: 153 minutes 41.55 seconds (9221.55 seconds total)