Starting phenix.real_space_refine on Fri May 9 14:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.map" model { file = "/net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j27_35946/05_2025/8j27_35946.cif" } resolution = 3.6 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= 0.001 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 8 5.16 5 C 1500 2.51 5 N 425 2.21 5 O 458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2393 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 99 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 138 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2001 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 3 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.94 Number of scatterers: 2393 At special positions: 0 Unit cell: (67.84, 68.9, 78.44, 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 8 16.00 P 2 15.00 O 458 8.00 N 425 7.00 C 1500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 259.7 milliseconds 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 54.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.511A pdb=" N LYS B 12 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.591A pdb=" N LEU B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.761A pdb=" N PHE B 128 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'E' and resid 79 through 85 removed outlier: 3.554A pdb=" N LYS E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 123 removed outlier: 3.932A pdb=" N ASN B 154 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 123 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 55 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N PHE B 153 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 57 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLU B 155 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE B 257 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 404 1.32 - 1.44: 617 1.44 - 1.56: 1382 1.56 - 1.68: 3 1.68 - 1.81: 14 Bond restraints: 2420 Sorted by residual: bond pdb=" C CYS B 95 " pdb=" O CYS B 95 " ideal model delta sigma weight residual 1.236 1.197 0.040 1.15e-02 7.56e+03 1.19e+01 bond pdb=" N ALA E 81 " pdb=" CA ALA E 81 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" C GLY B 97 " pdb=" O GLY B 97 " ideal model delta sigma weight residual 1.235 1.271 -0.037 1.35e-02 5.49e+03 7.41e+00 bond pdb=" C ALA B 94 " pdb=" O ALA B 94 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.28e-02 6.10e+03 7.37e+00 bond pdb=" N CYS B 95 " pdb=" CA CYS B 95 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.19e-02 7.06e+03 7.16e+00 ... (remaining 2415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 3010 1.56 - 3.13: 194 3.13 - 4.69: 37 4.69 - 6.25: 13 6.25 - 7.81: 3 Bond angle restraints: 3257 Sorted by residual: angle pdb=" N CYS B 95 " pdb=" CA CYS B 95 " pdb=" C CYS B 95 " ideal model delta sigma weight residual 111.07 104.19 6.88 1.07e+00 8.73e-01 4.13e+01 angle pdb=" N PHE F 80 " pdb=" CA PHE F 80 " pdb=" C PHE F 80 " ideal model delta sigma weight residual 111.75 103.94 7.81 1.28e+00 6.10e-01 3.73e+01 angle pdb=" N ALA B 81 " pdb=" CA ALA B 81 " pdb=" C ALA B 81 " ideal model delta sigma weight residual 112.87 106.75 6.12 1.20e+00 6.94e-01 2.60e+01 angle pdb=" C GLN B 100 " pdb=" N SER B 101 " pdb=" CA SER B 101 " ideal model delta sigma weight residual 120.54 113.99 6.55 1.35e+00 5.49e-01 2.36e+01 angle pdb=" N GLY B 64 " pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 112.50 117.73 -5.23 1.16e+00 7.43e-01 2.03e+01 ... (remaining 3252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 1343 25.68 - 51.35: 103 51.35 - 77.03: 6 77.03 - 102.70: 1 102.70 - 128.38: 2 Dihedral angle restraints: 1455 sinusoidal: 582 harmonic: 873 Sorted by residual: dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 68.38 -128.38 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 61.59 -121.59 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " pdb=" OD1 ASP B 115 " ideal model delta sinusoidal sigma weight residual -30.00 -87.59 57.59 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 1452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 197 0.028 - 0.056: 107 0.056 - 0.083: 40 0.083 - 0.111: 22 0.111 - 0.139: 13 Chirality restraints: 379 Sorted by residual: chirality pdb=" CA ILE B 56 " pdb=" N ILE B 56 " pdb=" C ILE B 56 " pdb=" CB ILE B 56 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 376 not shown) Planarity restraints: 411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 80 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C PHE B 80 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE B 80 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 81 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 43 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" CD GLU B 43 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU B 43 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 43 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 95 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C CYS B 95 " 0.019 2.00e-02 2.50e+03 pdb=" O CYS B 95 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA B 96 " -0.006 2.00e-02 2.50e+03 ... (remaining 408 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 543 2.77 - 3.30: 2473 3.30 - 3.83: 3799 3.83 - 4.37: 4318 4.37 - 4.90: 7019 Nonbonded interactions: 18152 Sorted by model distance: nonbonded pdb=" OG SER B 60 " pdb=" ND2 ASN B 176 " model vdw 2.233 3.120 nonbonded pdb=" OE2 GLU B 199 " pdb=" OH TYR B 202 " model vdw 2.294 3.040 nonbonded pdb=" N GLU B 199 " pdb=" OE1 GLU B 199 " model vdw 2.297 3.120 nonbonded pdb=" O SER F 79 " pdb=" N ASP F 82 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG B 134 " pdb=" OE1 GLU B 186 " model vdw 2.318 3.120 ... (remaining 18147 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' and resid 71 through 84) selection = (chain 'E' and resid 71 through 84) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.006 0.040 2420 Z= 0.420 Angle : 0.896 7.813 3257 Z= 0.590 Chirality : 0.047 0.139 379 Planarity : 0.003 0.020 411 Dihedral : 17.193 128.380 891 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.72 % Allowed : 31.89 % Favored : 63.39 % 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: -1.70 (0.47), residues: 293 helix: -1.19 (0.41), residues: 144 sheet: 1.21 (0.87), residues: 37 loop : -1.72 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 174 HIS 0.003 0.001 HIS B 281 PHE 0.011 0.002 PHE B 280 TYR 0.007 0.001 TYR B 107 ARG 0.002 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.20460 ( 106) hydrogen bonds : angle 7.66395 ( 291) covalent geometry : bond 0.00608 ( 2420) covalent geometry : angle 0.89624 ( 3257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 SER cc_start: 0.9393 (m) cc_final: 0.8955 (t) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 0.1348 time to fit residues: 15.1308 Evaluate side-chains 81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN B 120 GLN B 222 HIS B 223 GLN E 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094112 restraints weight = 7844.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096711 restraints weight = 4652.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098557 restraints weight = 3249.547| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2420 Z= 0.149 Angle : 0.722 6.441 3257 Z= 0.353 Chirality : 0.044 0.167 379 Planarity : 0.004 0.026 411 Dihedral : 10.906 117.721 347 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.12 % Allowed : 29.53 % Favored : 65.35 % 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: -0.57 (0.48), residues: 293 helix: 0.19 (0.44), residues: 134 sheet: 0.98 (0.86), residues: 39 loop : -1.46 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.021 0.002 PHE F 80 TYR 0.024 0.002 TYR E 72 ARG 0.003 0.001 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 106) hydrogen bonds : angle 4.84398 ( 291) covalent geometry : bond 0.00328 ( 2420) covalent geometry : angle 0.72220 ( 3257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.257 Fit side-chains REVERT: F 72 TYR cc_start: 0.7746 (t80) cc_final: 0.7476 (t80) REVERT: A 78 SER cc_start: 0.9210 (m) cc_final: 0.8892 (t) REVERT: B 72 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 144 MET cc_start: 0.9220 (ttt) cc_final: 0.8568 (tmm) REVERT: B 225 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8350 (pp20) outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.1048 time to fit residues: 10.8660 Evaluate side-chains 76 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain E residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088955 restraints weight = 8192.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091444 restraints weight = 4774.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093183 restraints weight = 3315.683| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2420 Z= 0.242 Angle : 0.785 5.993 3257 Z= 0.385 Chirality : 0.045 0.160 379 Planarity : 0.004 0.025 411 Dihedral : 10.829 119.527 344 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 8.66 % Allowed : 31.10 % Favored : 60.24 % 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: -0.53 (0.46), residues: 293 helix: 0.36 (0.41), residues: 135 sheet: 1.11 (0.88), residues: 39 loop : -1.69 (0.52), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.002 PHE B 173 TYR 0.010 0.002 TYR B 72 ARG 0.004 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 106) hydrogen bonds : angle 4.87907 ( 291) covalent geometry : bond 0.00527 ( 2420) covalent geometry : angle 0.78546 ( 3257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 78 SER cc_start: 0.9381 (m) cc_final: 0.9158 (t) REVERT: B 44 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8851 (pp30) REVERT: B 72 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7713 (t80) REVERT: B 139 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8644 (tm-30) REVERT: B 144 MET cc_start: 0.9265 (ttt) cc_final: 0.8600 (tmm) REVERT: B 156 ASN cc_start: 0.8151 (t0) cc_final: 0.7764 (t0) REVERT: B 225 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8267 (pp20) outliers start: 22 outliers final: 11 residues processed: 87 average time/residue: 0.1116 time to fit residues: 11.7806 Evaluate side-chains 78 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092567 restraints weight = 7820.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095194 restraints weight = 4635.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096942 restraints weight = 3185.830| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2420 Z= 0.129 Angle : 0.741 8.445 3257 Z= 0.345 Chirality : 0.044 0.154 379 Planarity : 0.003 0.015 411 Dihedral : 10.380 112.344 342 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.09 % Allowed : 28.35 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.48), residues: 293 helix: 0.71 (0.42), residues: 137 sheet: 1.00 (0.90), residues: 40 loop : -1.69 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.011 0.001 PHE B 80 TYR 0.015 0.001 TYR F 72 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 106) hydrogen bonds : angle 4.63582 ( 291) covalent geometry : bond 0.00286 ( 2420) covalent geometry : angle 0.74092 ( 3257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9265 (tp30) cc_final: 0.9064 (tp30) REVERT: B 44 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8858 (pp30) REVERT: B 72 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7755 (t80) REVERT: B 144 MET cc_start: 0.9130 (ttt) cc_final: 0.8580 (tmm) REVERT: B 225 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8378 (pp20) REVERT: B 266 ASN cc_start: 0.9075 (m110) cc_final: 0.8867 (m110) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.1033 time to fit residues: 10.5184 Evaluate side-chains 83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090988 restraints weight = 8205.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093567 restraints weight = 4865.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095326 restraints weight = 3349.848| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2420 Z= 0.169 Angle : 0.754 7.925 3257 Z= 0.353 Chirality : 0.043 0.149 379 Planarity : 0.003 0.017 411 Dihedral : 10.188 110.080 342 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 7.48 % Allowed : 31.50 % Favored : 61.02 % 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: -0.22 (0.49), residues: 293 helix: 0.80 (0.42), residues: 137 sheet: 1.17 (0.92), residues: 40 loop : -1.82 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.007 0.001 PHE B 153 TYR 0.006 0.001 TYR F 72 ARG 0.002 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 106) hydrogen bonds : angle 4.58720 ( 291) covalent geometry : bond 0.00379 ( 2420) covalent geometry : angle 0.75413 ( 3257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9265 (tp30) cc_final: 0.9061 (tp30) REVERT: B 44 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8880 (pp30) REVERT: B 72 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7854 (t80) REVERT: B 139 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8692 (tm-30) REVERT: B 144 MET cc_start: 0.9195 (ttt) cc_final: 0.8596 (tmm) REVERT: B 225 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8431 (pp20) REVERT: B 266 ASN cc_start: 0.9191 (m110) cc_final: 0.8965 (m110) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.1088 time to fit residues: 11.0195 Evaluate side-chains 83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.092256 restraints weight = 8044.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094894 restraints weight = 4866.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096706 restraints weight = 3369.190| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2420 Z= 0.137 Angle : 0.741 7.365 3257 Z= 0.345 Chirality : 0.043 0.150 379 Planarity : 0.003 0.015 411 Dihedral : 9.918 102.311 342 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.30 % Allowed : 34.25 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.50), residues: 293 helix: 0.88 (0.44), residues: 137 sheet: 1.20 (0.93), residues: 40 loop : -1.83 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.011 0.001 PHE F 80 TYR 0.007 0.001 TYR E 72 ARG 0.002 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 106) hydrogen bonds : angle 4.59814 ( 291) covalent geometry : bond 0.00310 ( 2420) covalent geometry : angle 0.74126 ( 3257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9263 (tp30) cc_final: 0.9029 (tp30) REVERT: B 44 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8854 (pp30) REVERT: B 72 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7859 (t80) REVERT: B 102 SER cc_start: 0.9523 (m) cc_final: 0.9213 (t) REVERT: B 144 MET cc_start: 0.9161 (ttt) cc_final: 0.8610 (tmm) REVERT: B 266 ASN cc_start: 0.9134 (m110) cc_final: 0.8921 (m110) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.1083 time to fit residues: 10.4764 Evaluate side-chains 84 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091856 restraints weight = 8238.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094402 restraints weight = 5074.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096200 restraints weight = 3569.510| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2420 Z= 0.149 Angle : 0.755 6.376 3257 Z= 0.353 Chirality : 0.043 0.155 379 Planarity : 0.003 0.015 411 Dihedral : 9.659 89.290 342 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 7.09 % Allowed : 35.43 % Favored : 57.48 % 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: -0.11 (0.50), residues: 293 helix: 0.95 (0.44), residues: 137 sheet: 1.27 (0.94), residues: 40 loop : -1.88 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.001 PHE B 153 TYR 0.018 0.001 TYR E 72 ARG 0.004 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 106) hydrogen bonds : angle 4.58997 ( 291) covalent geometry : bond 0.00340 ( 2420) covalent geometry : angle 0.75495 ( 3257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9313 (tp30) cc_final: 0.9057 (tp30) REVERT: B 44 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8853 (pp30) REVERT: B 72 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 110 MET cc_start: 0.6421 (tpt) cc_final: 0.6160 (ttm) REVERT: B 139 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8890 (tm-30) REVERT: B 144 MET cc_start: 0.9224 (ttt) cc_final: 0.8638 (tmm) REVERT: B 266 ASN cc_start: 0.9197 (m110) cc_final: 0.8975 (m110) outliers start: 18 outliers final: 15 residues processed: 78 average time/residue: 0.1104 time to fit residues: 10.5507 Evaluate side-chains 82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091595 restraints weight = 8472.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094203 restraints weight = 5117.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.095980 restraints weight = 3564.929| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2420 Z= 0.148 Angle : 0.746 6.603 3257 Z= 0.350 Chirality : 0.043 0.149 379 Planarity : 0.003 0.015 411 Dihedral : 9.653 112.415 342 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 7.87 % Allowed : 33.07 % Favored : 59.06 % 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: 0.04 (0.51), residues: 293 helix: 1.02 (0.44), residues: 136 sheet: 1.29 (0.95), residues: 40 loop : -1.67 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.012 0.001 PHE F 80 TYR 0.007 0.001 TYR F 72 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 106) hydrogen bonds : angle 4.62196 ( 291) covalent geometry : bond 0.00337 ( 2420) covalent geometry : angle 0.74629 ( 3257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9319 (tp30) cc_final: 0.9058 (tp30) REVERT: B 44 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8859 (pp30) REVERT: B 72 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7861 (t80) REVERT: B 120 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8458 (pp30) REVERT: B 139 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8748 (tm-30) REVERT: B 144 MET cc_start: 0.9190 (ttt) cc_final: 0.8559 (tmm) REVERT: B 266 ASN cc_start: 0.9210 (m110) cc_final: 0.8978 (m110) outliers start: 20 outliers final: 15 residues processed: 80 average time/residue: 0.1139 time to fit residues: 11.1388 Evaluate side-chains 84 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092265 restraints weight = 8162.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094801 restraints weight = 5026.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096576 restraints weight = 3530.196| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2420 Z= 0.140 Angle : 0.767 7.638 3257 Z= 0.356 Chirality : 0.042 0.145 379 Planarity : 0.003 0.014 411 Dihedral : 9.754 126.117 342 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.30 % Allowed : 37.40 % Favored : 56.30 % 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: 0.04 (0.51), residues: 293 helix: 1.05 (0.45), residues: 136 sheet: 1.29 (0.94), residues: 40 loop : -1.72 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.001 PHE B 153 TYR 0.027 0.002 TYR E 72 ARG 0.004 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 106) hydrogen bonds : angle 4.59361 ( 291) covalent geometry : bond 0.00323 ( 2420) covalent geometry : angle 0.76655 ( 3257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9302 (tp30) cc_final: 0.9053 (tp30) REVERT: B 44 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8855 (pp30) REVERT: B 72 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 120 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8404 (pp30) REVERT: B 139 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8713 (tm-30) REVERT: B 144 MET cc_start: 0.9155 (ttt) cc_final: 0.8593 (tmm) REVERT: B 266 ASN cc_start: 0.9186 (m110) cc_final: 0.8955 (m110) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.1062 time to fit residues: 10.5733 Evaluate side-chains 82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN E 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092799 restraints weight = 8269.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095367 restraints weight = 5023.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097177 restraints weight = 3495.822| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2420 Z= 0.137 Angle : 0.795 7.813 3257 Z= 0.371 Chirality : 0.043 0.155 379 Planarity : 0.003 0.021 411 Dihedral : 9.758 129.224 342 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.69 % Allowed : 38.19 % Favored : 55.12 % 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: -0.03 (0.50), residues: 293 helix: 1.03 (0.44), residues: 137 sheet: 1.27 (0.92), residues: 40 loop : -1.84 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.002 0.000 HIS B 281 PHE 0.013 0.001 PHE F 80 TYR 0.008 0.001 TYR F 72 ARG 0.005 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 106) hydrogen bonds : angle 4.64151 ( 291) covalent geometry : bond 0.00322 ( 2420) covalent geometry : angle 0.79533 ( 3257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9310 (tp30) cc_final: 0.9069 (tp30) REVERT: B 44 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8848 (pp30) REVERT: B 72 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7856 (t80) REVERT: B 120 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8408 (pp30) REVERT: B 139 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8694 (tm-30) REVERT: B 144 MET cc_start: 0.9144 (ttt) cc_final: 0.8580 (tmm) REVERT: B 266 ASN cc_start: 0.9159 (m110) cc_final: 0.8939 (m110) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.1076 time to fit residues: 10.4157 Evaluate side-chains 84 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.105859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090986 restraints weight = 8305.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093508 restraints weight = 5024.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095245 restraints weight = 3489.613| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2420 Z= 0.169 Angle : 0.798 7.850 3257 Z= 0.376 Chirality : 0.043 0.154 379 Planarity : 0.003 0.018 411 Dihedral : 9.851 132.796 342 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 7.09 % Allowed : 37.80 % Favored : 55.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.50), residues: 293 helix: 1.00 (0.44), residues: 136 sheet: 1.27 (0.92), residues: 40 loop : -1.73 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.007 0.001 PHE E 80 TYR 0.028 0.002 TYR E 72 ARG 0.005 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 106) hydrogen bonds : angle 4.63325 ( 291) covalent geometry : bond 0.00392 ( 2420) covalent geometry : angle 0.79848 ( 3257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1206.68 seconds wall clock time: 22 minutes 6.61 seconds (1326.61 seconds total)