Starting phenix.real_space_refine on Wed Mar 5 15:40:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j27_35946/03_2025/8j27_35946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j27_35946/03_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_35946/03_2025/8j27_35946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j27_35946/03_2025/8j27_35946.map" model { file = "/net/cci-nas-00/data/ceres_data/8j27_35946/03_2025/8j27_35946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j27_35946/03_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-5624/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: 2.42, per 1000 atoms: 1.01 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: 0.75 Conformation dependent library (CDL) restraints added in 294.2 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: 0.55 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: 0.61 Time building geometry restraints manager: 0.79 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: 0.700 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.990 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- 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= 0.390 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 *********************** 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 : 0.255 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: 0.1378 time to fit residues: 15.5201 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 : 0.263 ------------------------------------------------------------------------------- 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 = 0.094109 restraints weight = 7844.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096714 restraints weight = 4654.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098557 restraints weight = 3241.162| |-----------------------------------------------------------------------------| 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= 0.213 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 *********************** 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 : 0.265 Fit side-chains REVERT: F 72 TYR cc_start: 0.7746 (t80) cc_final: 0.7475 (t80) REVERT: A 78 SER cc_start: 0.9211 (m) cc_final: 0.8892 (t) REVERT: B 72 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 144 MET cc_start: 0.9219 (ttt) cc_final: 0.8566 (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: 0.1041 time to fit residues: 10.8268 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 : 0.264 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.106012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091129 restraints weight = 8106.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093626 restraints weight = 4749.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095449 restraints weight = 3295.532| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2420 Z= 0.278 Angle : 0.751 6.053 3257 Z= 0.363 Chirality : 0.044 0.179 379 Planarity : 0.004 0.021 411 Dihedral : 10.684 117.418 344 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.69 % Allowed : 32.28 % 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: -0.39 (0.47), residues: 293 helix: 0.49 (0.41), residues: 135 sheet: 1.03 (0.89), residues: 40 loop : -1.60 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.007 0.001 PHE B 10 TYR 0.007 0.001 TYR B 72 ARG 0.005 0.001 ARG A 71 *********************** 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 88 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: F 72 TYR cc_start: 0.7966 (t80) cc_final: 0.7738 (t80) REVERT: A 78 SER cc_start: 0.9375 (m) cc_final: 0.9163 (t) REVERT: B 44 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8803 (pp30) REVERT: B 72 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 144 MET cc_start: 0.9272 (ttt) cc_final: 0.8608 (tmm) REVERT: B 156 ASN cc_start: 0.8098 (t0) cc_final: 0.7695 (t0) REVERT: E 72 TYR cc_start: 0.8149 (t80) cc_final: 0.7859 (t80) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 0.1173 time to fit residues: 11.7102 Evaluate side-chains 80 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.107267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.092135 restraints weight = 7888.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094711 restraints weight = 4692.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096566 restraints weight = 3248.521| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2420 Z= 0.209 Angle : 0.750 7.612 3257 Z= 0.345 Chirality : 0.043 0.152 379 Planarity : 0.003 0.017 411 Dihedral : 10.380 112.888 342 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.30 % Allowed : 30.31 % 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: -0.21 (0.48), residues: 293 helix: 0.74 (0.41), residues: 137 sheet: 1.07 (0.90), residues: 40 loop : -1.66 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.001 PHE F 80 TYR 0.004 0.001 TYR B 106 ARG 0.003 0.000 ARG A 71 *********************** 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 90 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9273 (tp30) cc_final: 0.9070 (tp30) REVERT: B 44 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8880 (pp30) REVERT: B 72 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7748 (t80) REVERT: B 144 MET cc_start: 0.9188 (ttt) cc_final: 0.8577 (tmm) REVERT: B 225 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8320 (pp20) REVERT: B 266 ASN cc_start: 0.9097 (m110) cc_final: 0.8887 (m110) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.1051 time to fit residues: 10.7616 Evaluate side-chains 85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 57 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 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: 7.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.106169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091194 restraints weight = 8177.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093726 restraints weight = 4910.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095492 restraints weight = 3427.294| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2420 Z= 0.227 Angle : 0.741 6.647 3257 Z= 0.347 Chirality : 0.043 0.150 379 Planarity : 0.003 0.020 411 Dihedral : 10.144 109.697 342 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 8.27 % Allowed : 29.53 % Favored : 62.20 % 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: -0.10 (0.49), residues: 293 helix: 0.88 (0.42), residues: 137 sheet: 1.26 (0.92), residues: 40 loop : -1.74 (0.54), 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 0.005 0.001 PHE B 10 TYR 0.011 0.001 TYR F 72 ARG 0.003 0.000 ARG A 71 *********************** 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 91 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9266 (tp30) cc_final: 0.9058 (tp30) REVERT: B 44 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8853 (pp30) REVERT: B 72 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 139 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 144 MET cc_start: 0.9204 (ttt) cc_final: 0.8599 (tmm) REVERT: B 266 ASN cc_start: 0.9178 (m110) cc_final: 0.8975 (m110) outliers start: 21 outliers final: 14 residues processed: 82 average time/residue: 0.1127 time to fit residues: 11.5192 Evaluate side-chains 83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 214 ILE 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: 3.9990 chunk 13 optimal weight: 0.0370 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 0.0030 overall best weight: 1.2072 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.107387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092250 restraints weight = 8093.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094889 restraints weight = 4867.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096606 restraints weight = 3372.137| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2420 Z= 0.209 Angle : 0.746 6.788 3257 Z= 0.346 Chirality : 0.043 0.149 379 Planarity : 0.003 0.019 411 Dihedral : 9.894 102.095 342 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 7.09 % Allowed : 33.46 % 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: -0.03 (0.49), residues: 293 helix: 1.00 (0.43), residues: 137 sheet: 1.24 (0.93), residues: 40 loop : -1.79 (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 0.011 0.001 PHE F 80 TYR 0.009 0.001 TYR F 72 ARG 0.003 0.000 ARG A 71 *********************** 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 89 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9269 (tp30) cc_final: 0.9036 (tp30) REVERT: B 44 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8847 (pp30) REVERT: B 72 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 102 SER cc_start: 0.9527 (m) cc_final: 0.9002 (t) REVERT: B 139 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8707 (tm-30) REVERT: B 144 MET cc_start: 0.9144 (ttt) cc_final: 0.8633 (tmm) REVERT: B 266 ASN cc_start: 0.9134 (m110) cc_final: 0.8926 (m110) outliers start: 18 outliers final: 14 residues processed: 79 average time/residue: 0.1137 time to fit residues: 11.1763 Evaluate side-chains 85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 57 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 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 214 ILE 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: 0.0010 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 overall best weight: 0.7506 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094139 restraints weight = 8052.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096813 restraints weight = 4853.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098630 restraints weight = 3382.511| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4839 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= 0.191 Angle : 0.742 6.415 3257 Z= 0.345 Chirality : 0.043 0.151 379 Planarity : 0.002 0.016 411 Dihedral : 9.504 85.654 342 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.91 % Allowed : 35.04 % 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: 0.02 (0.50), residues: 293 helix: 1.04 (0.44), residues: 137 sheet: 1.33 (0.94), residues: 40 loop : -1.79 (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 0.005 0.001 PHE E 80 TYR 0.012 0.001 TYR E 72 ARG 0.004 0.000 ARG A 71 *********************** 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 87 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9285 (tp30) cc_final: 0.9049 (tp30) REVERT: B 44 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8829 (pp30) REVERT: B 72 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 110 MET cc_start: 0.6419 (tpt) cc_final: 0.6194 (ttm) REVERT: B 144 MET cc_start: 0.9171 (ttt) cc_final: 0.8639 (tmm) REVERT: B 266 ASN cc_start: 0.9100 (m110) cc_final: 0.8900 (m110) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.1088 time to fit residues: 10.8327 Evaluate side-chains 82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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 182 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 240 THR 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: 9.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091133 restraints weight = 8612.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093687 restraints weight = 5235.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095493 restraints weight = 3659.558| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2420 Z= 0.257 Angle : 0.790 9.026 3257 Z= 0.369 Chirality : 0.044 0.179 379 Planarity : 0.003 0.019 411 Dihedral : 9.527 107.716 342 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 7.48 % Allowed : 35.43 % Favored : 57.09 % 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: 0.08 (0.51), residues: 293 helix: 1.04 (0.44), residues: 136 sheet: 1.33 (0.95), residues: 40 loop : -1.64 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.003 0.001 HIS B 281 PHE 0.012 0.001 PHE F 80 TYR 0.028 0.002 TYR E 72 ARG 0.005 0.000 ARG A 71 *********************** 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 83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9316 (tp30) cc_final: 0.9059 (tp30) REVERT: B 44 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8849 (pp30) REVERT: B 72 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7942 (t80) REVERT: B 139 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8873 (tm-30) REVERT: B 144 MET cc_start: 0.9215 (ttt) cc_final: 0.8642 (tmm) REVERT: B 266 ASN cc_start: 0.9204 (m110) cc_final: 0.8984 (m110) outliers start: 19 outliers final: 15 residues processed: 75 average time/residue: 0.1131 time to fit residues: 10.4299 Evaluate side-chains 79 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 57 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 182 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 225 GLU 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: 3.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091007 restraints weight = 8194.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093504 restraints weight = 4961.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095227 restraints weight = 3474.430| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2420 Z= 0.270 Angle : 0.798 8.580 3257 Z= 0.374 Chirality : 0.043 0.147 379 Planarity : 0.003 0.021 411 Dihedral : 9.745 123.968 342 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.30 % Allowed : 36.22 % 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: 0.05 (0.50), residues: 293 helix: 1.02 (0.44), residues: 136 sheet: 1.35 (0.94), residues: 40 loop : -1.68 (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 B 10 TYR 0.006 0.001 TYR E 72 ARG 0.004 0.000 ARG A 71 *********************** 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 80 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9312 (tp30) cc_final: 0.9060 (tp30) REVERT: B 44 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8872 (pp30) REVERT: B 72 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 139 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8853 (tm-30) REVERT: B 144 MET cc_start: 0.9235 (ttt) cc_final: 0.8654 (tmm) REVERT: B 266 ASN cc_start: 0.9239 (m110) cc_final: 0.9008 (m110) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.1106 time to fit residues: 9.9228 Evaluate side-chains 77 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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 182 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE 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: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.0170 overall best weight: 0.5022 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.094198 restraints weight = 8365.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096881 restraints weight = 5137.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098714 restraints weight = 3612.655| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2420 Z= 0.209 Angle : 0.799 9.475 3257 Z= 0.366 Chirality : 0.042 0.146 379 Planarity : 0.002 0.015 411 Dihedral : 9.912 132.266 342 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.72 % Allowed : 38.19 % Favored : 57.09 % 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: 0.10 (0.50), residues: 293 helix: 1.10 (0.45), residues: 136 sheet: 1.36 (0.94), residues: 40 loop : -1.70 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.013 0.001 PHE F 80 TYR 0.020 0.001 TYR E 72 ARG 0.004 0.000 ARG A 71 ********************** 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 81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.9268 (tp30) cc_final: 0.9024 (tp30) REVERT: B 44 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8828 (pp30) REVERT: B 72 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 110 MET cc_start: 0.7106 (tpt) cc_final: 0.6669 (ttm) REVERT: B 139 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 144 MET cc_start: 0.9110 (ttt) cc_final: 0.8565 (tmm) REVERT: B 266 ASN cc_start: 0.9097 (m110) cc_final: 0.8875 (m110) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.1129 time to fit residues: 10.5123 Evaluate side-chains 79 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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 182 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 240 THR 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: 3.9990 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 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 84 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 = 0.3726 r_free = 0.3726 target = 0.109420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093888 restraints weight = 8226.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096510 restraints weight = 5092.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098283 restraints weight = 3590.078| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2420 Z= 0.215 Angle : 0.776 7.679 3257 Z= 0.358 Chirality : 0.042 0.141 379 Planarity : 0.002 0.012 411 Dihedral : 9.787 131.402 342 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.94 % Allowed : 38.98 % Favored : 57.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.51), residues: 293 helix: 1.13 (0.45), residues: 136 sheet: 1.40 (0.95), residues: 40 loop : -1.69 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.014 0.001 PHE A 80 TYR 0.004 0.001 TYR A 72 ARG 0.004 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.12 seconds wall clock time: 22 minutes 24.48 seconds (1344.48 seconds total)