Starting phenix.real_space_refine on Wed Nov 13 23:52:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_35946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_35946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_35946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_35946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j27_35946/11_2024/8j27_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-5513/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: 2.34, per 1000 atoms: 0.98 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 304.4 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: 0.30 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: 0.59 Time building geometry restraints manager: 0.78 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: 0.610 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.580 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- 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 : 0.257 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: 0.1419 time to fit residues: 15.8442 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 : 0.259 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.336 Fit side-chains REVERT: F 72 TYR cc_start: 0.7683 (t80) cc_final: 0.7201 (t80) REVERT: A 78 SER cc_start: 0.9403 (m) cc_final: 0.9101 (t) REVERT: B 72 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6772 (t80) outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.1143 time to fit residues: 11.7361 Evaluate side-chains 75 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2420 Z= 0.344 Angle : 0.792 5.989 3257 Z= 0.389 Chirality : 0.045 0.157 379 Planarity : 0.004 0.026 411 Dihedral : 10.860 119.683 344 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 8.27 % Allowed : 31.50 % 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: -0.60 (0.46), residues: 293 helix: 0.31 (0.41), residues: 135 sheet: 1.07 (0.87), residues: 39 loop : -1.74 (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 *********************** 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 89 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7161 (t80) REVERT: B 139 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 156 ASN cc_start: 0.8162 (t0) cc_final: 0.7957 (t0) outliers start: 21 outliers final: 12 residues processed: 84 average time/residue: 0.1135 time to fit residues: 11.5308 Evaluate side-chains 77 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU 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 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3963 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= 0.183 Angle : 0.732 7.038 3257 Z= 0.344 Chirality : 0.044 0.159 379 Planarity : 0.003 0.015 411 Dihedral : 10.366 112.013 342 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 7.48 % Allowed : 29.13 % 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: -0.30 (0.48), residues: 293 helix: 0.66 (0.41), residues: 137 sheet: 1.02 (0.91), residues: 40 loop : -1.70 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.001 0.000 HIS B 281 PHE 0.010 0.001 PHE B 80 TYR 0.016 0.001 TYR F 72 ARG 0.002 0.000 ARG E 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: 19 poor density : 71 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7157 (t80) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1139 time to fit residues: 11.3809 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 : 0.260 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2420 Z= 0.212 Angle : 0.785 8.886 3257 Z= 0.364 Chirality : 0.044 0.156 379 Planarity : 0.003 0.015 411 Dihedral : 10.056 107.912 342 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.30 % Allowed : 33.07 % Favored : 60.63 % 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: -0.38 (0.48), residues: 293 helix: 0.63 (0.42), residues: 137 sheet: 1.20 (0.91), residues: 40 loop : -1.89 (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 0.009 0.001 PHE B 153 TYR 0.009 0.001 TYR F 72 ARG 0.002 0.000 ARG A 69 *********************** 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 87 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.1105 time to fit residues: 10.8477 Evaluate side-chains 81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 17 ILE 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 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 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 28 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2420 Z= 0.287 Angle : 0.794 6.904 3257 Z= 0.377 Chirality : 0.045 0.149 379 Planarity : 0.003 0.017 411 Dihedral : 10.166 105.187 342 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 7.48 % Allowed : 33.46 % 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: -0.50 (0.49), residues: 293 helix: 0.57 (0.42), residues: 137 sheet: 1.03 (0.93), residues: 40 loop : -1.96 (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 0.010 0.001 PHE F 80 TYR 0.008 0.002 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 85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7258 (t80) REVERT: B 102 SER cc_start: 0.8682 (m) cc_final: 0.8179 (t) REVERT: B 214 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7753 (mt) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.1215 time to fit residues: 11.7482 Evaluate side-chains 78 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2420 Z= 0.208 Angle : 0.794 6.962 3257 Z= 0.371 Chirality : 0.044 0.159 379 Planarity : 0.003 0.016 411 Dihedral : 9.765 98.657 342 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.91 % Allowed : 35.83 % Favored : 58.27 % 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: -0.36 (0.49), residues: 293 helix: 0.68 (0.44), residues: 137 sheet: 1.08 (0.93), residues: 40 loop : -1.89 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 174 HIS 0.001 0.001 HIS B 281 PHE 0.008 0.001 PHE B 80 TYR 0.006 0.001 TYR F 72 ARG 0.002 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 81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.1061 time to fit residues: 9.9969 Evaluate side-chains 74 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 ASP 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 126 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2420 Z= 0.203 Angle : 0.823 7.305 3257 Z= 0.379 Chirality : 0.044 0.153 379 Planarity : 0.003 0.017 411 Dihedral : 9.621 115.715 342 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.51 % Allowed : 38.19 % 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: -0.29 (0.50), residues: 293 helix: 0.75 (0.44), residues: 137 sheet: 1.12 (0.92), residues: 40 loop : -1.86 (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 0.012 0.001 PHE F 80 TYR 0.016 0.001 TYR B 106 ARG 0.003 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 80 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7162 (t80) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.0984 time to fit residues: 9.3057 Evaluate side-chains 76 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 126 SER 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 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2420 Z= 0.225 Angle : 0.823 7.356 3257 Z= 0.385 Chirality : 0.044 0.148 379 Planarity : 0.003 0.020 411 Dihedral : 9.663 121.620 342 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.51 % Allowed : 37.80 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.50), residues: 293 helix: 0.54 (0.44), residues: 138 sheet: 1.28 (0.93), residues: 40 loop : -1.84 (0.57), residues: 115 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 0.027 0.002 TYR E 72 ARG 0.006 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 82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7060 (t80) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.1033 time to fit residues: 9.7636 Evaluate side-chains 78 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 126 SER 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 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.0050 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5350 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= 0.228 Angle : 0.842 7.724 3257 Z= 0.394 Chirality : 0.044 0.151 379 Planarity : 0.003 0.019 411 Dihedral : 9.854 128.971 342 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.94 % Allowed : 40.55 % Favored : 55.51 % 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: -0.45 (0.50), residues: 293 helix: 0.46 (0.43), residues: 138 sheet: 1.21 (0.93), residues: 40 loop : -1.80 (0.57), residues: 115 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 0.012 0.002 PHE F 80 TYR 0.035 0.002 TYR B 106 ARG 0.006 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 77 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 72 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7117 (t80) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.1018 time to fit residues: 9.3401 Evaluate side-chains 74 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 126 SER 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 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.109485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.094025 restraints weight = 8097.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096618 restraints weight = 5012.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098415 restraints weight = 3549.561| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2420 Z= 0.216 Angle : 0.833 7.778 3257 Z= 0.387 Chirality : 0.043 0.146 379 Planarity : 0.003 0.023 411 Dihedral : 9.826 131.042 342 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.33 % Allowed : 40.16 % Favored : 55.51 % 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: -0.52 (0.49), residues: 293 helix: 0.38 (0.43), residues: 138 sheet: 1.33 (0.93), residues: 40 loop : -1.88 (0.56), residues: 115 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 0.010 0.001 PHE E 80 TYR 0.023 0.002 TYR E 72 ARG 0.005 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.87 seconds wall clock time: 19 minutes 26.65 seconds (1166.65 seconds total)