Starting phenix.real_space_refine on Sun Mar 10 18:26:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/03_2024/7d4g_30573.pdb" } resolution = 3.9 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= 0.002 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2510 2.51 5 N 648 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3925 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2206 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Time building chain proxies: 2.60, per 1000 atoms: 0.66 Number of scatterers: 3925 At special positions: 0 Unit cell: (60.32, 99.84, 90.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 752 8.00 N 648 7.00 C 2510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.51 Conformation dependent library (CDL) restraints added in 862.0 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 11 sheets defined 2.6% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU G 84 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.087A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.918A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.813A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR G 91 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL G 100 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 20 through 23 Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.836A pdb=" N GLN N 3 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA N 80 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 46 through 49 109 hydrogen bonds defined for protein. 264 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: 0.96 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1217 1.34 - 1.46: 914 1.46 - 1.58: 1876 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4029 Sorted by residual: bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.34e-02 1.83e+03 1.72e+01 bond pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N ILE B 285 " pdb=" CA ILE B 285 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N ILE B 203 " pdb=" CA ILE B 203 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.50e+00 bond pdb=" N VAL B 42 " pdb=" CA VAL B 42 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.32e+00 ... (remaining 4024 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 141 106.75 - 113.55: 2156 113.55 - 120.36: 1441 120.36 - 127.17: 1696 127.17 - 133.98: 51 Bond angle restraints: 5485 Sorted by residual: angle pdb=" N ALA B 123 " pdb=" CA ALA B 123 " pdb=" C ALA B 123 " ideal model delta sigma weight residual 107.57 125.63 -18.06 1.94e+00 2.66e-01 8.66e+01 angle pdb=" N THR B 124 " pdb=" CA THR B 124 " pdb=" C THR B 124 " ideal model delta sigma weight residual 111.71 102.70 9.01 1.15e+00 7.56e-01 6.14e+01 angle pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta sigma weight residual 120.28 109.69 10.59 1.44e+00 4.82e-01 5.41e+01 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 110.97 118.64 -7.67 1.56e+00 4.11e-01 2.42e+01 angle pdb=" N THR N 101 " pdb=" CA THR N 101 " pdb=" C THR N 101 " ideal model delta sigma weight residual 109.64 115.61 -5.97 1.27e+00 6.20e-01 2.21e+01 ... (remaining 5480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 2256 16.12 - 32.23: 72 32.23 - 48.35: 19 48.35 - 64.46: 1 64.46 - 80.58: 4 Dihedral angle restraints: 2352 sinusoidal: 908 harmonic: 1444 Sorted by residual: dihedral pdb=" CA TYR B 248 " pdb=" C TYR B 248 " pdb=" N LEU B 249 " pdb=" CA LEU B 249 " ideal model delta harmonic sigma weight residual -180.00 -141.81 -38.19 0 5.00e+00 4.00e-02 5.83e+01 dihedral pdb=" CA SER N 8 " pdb=" C SER N 8 " pdb=" N GLY N 9 " pdb=" CA GLY N 9 " ideal model delta harmonic sigma weight residual -180.00 -144.92 -35.08 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA ALA B 123 " pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 2349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 544 0.095 - 0.190: 56 0.190 - 0.285: 1 0.285 - 0.380: 0 0.380 - 0.476: 2 Chirality restraints: 603 Sorted by residual: chirality pdb=" CA SER N 104 " pdb=" N SER N 104 " pdb=" C SER N 104 " pdb=" CB SER N 104 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA LEU B 276 " pdb=" N LEU B 276 " pdb=" C LEU B 276 " pdb=" CB LEU B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 600 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 122 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ASN B 122 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN B 122 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA B 123 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 120 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C VAL B 120 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL B 120 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO N 102 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C PRO N 102 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO N 102 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE N 103 " 0.013 2.00e-02 2.50e+03 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 56 2.51 - 3.11: 3143 3.11 - 3.71: 6126 3.71 - 4.30: 8710 4.30 - 4.90: 14193 Nonbonded interactions: 32228 Sorted by model distance: nonbonded pdb=" O GLU N 32 " pdb=" CG PRO N 102 " model vdw 1.917 3.440 nonbonded pdb=" O ASP N 91 " pdb=" OH TYR N 95 " model vdw 2.119 2.440 nonbonded pdb=" O GLU N 32 " pdb=" CB PRO N 102 " model vdw 2.123 3.440 nonbonded pdb=" NH1 ARG B 273 " pdb=" OD2 ASP B 290 " model vdw 2.126 2.520 nonbonded pdb=" CB PRO N 54 " pdb=" CB SER N 104 " model vdw 2.132 3.840 ... (remaining 32223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.370 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: 6.920 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 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 0.097 4029 Z= 0.395 Angle : 1.065 18.058 5485 Z= 0.654 Chirality : 0.061 0.476 603 Planarity : 0.006 0.044 703 Dihedral : 9.868 80.579 1420 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 36.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.73 % Favored : 88.87 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.29), residues: 494 helix: -4.21 (0.49), residues: 6 sheet: -1.91 (0.36), residues: 126 loop : -3.00 (0.26), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP B 64 HIS 0.007 0.002 HIS N 36 PHE 0.027 0.003 PHE B 106 TYR 0.018 0.002 TYR N 28 ARG 0.003 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6522 (tmm-80) REVERT: B 80 ASP cc_start: 0.7559 (t70) cc_final: 0.7359 (t0) REVERT: N 39 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7178 (mtp180) REVERT: N 55 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7106 (mt-10) REVERT: N 82 MET cc_start: 0.7286 (ttp) cc_final: 0.7071 (ttp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1803 time to fit residues: 31.6137 Evaluate side-chains 95 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN G 6 GLN G 39 GLN G 80 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4029 Z= 0.249 Angle : 0.823 11.416 5485 Z= 0.422 Chirality : 0.047 0.208 603 Planarity : 0.005 0.039 703 Dihedral : 7.316 44.858 541 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.89 % Rotamer: Outliers : 4.17 % Allowed : 13.19 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.31), residues: 494 helix: None (None), residues: 0 sheet: -1.30 (0.37), residues: 143 loop : -2.81 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP N 112 HIS 0.005 0.002 HIS B 49 PHE 0.031 0.003 PHE B 106 TYR 0.025 0.002 TYR G 88 ARG 0.004 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6670 (mm-40) cc_final: 0.6397 (mm110) REVERT: B 129 LYS cc_start: 0.7673 (mttt) cc_final: 0.7458 (ttmt) REVERT: B 168 PHE cc_start: 0.6470 (t80) cc_final: 0.6200 (t80) REVERT: B 177 MET cc_start: 0.5469 (ppp) cc_final: 0.4681 (mtp) REVERT: B 214 ARG cc_start: 0.6618 (mtp-110) cc_final: 0.6157 (ptm-80) REVERT: B 224 GLU cc_start: 0.7939 (pm20) cc_final: 0.7587 (pm20) REVERT: B 287 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5516 (m-30) REVERT: N 53 ASP cc_start: 0.8220 (t0) cc_final: 0.8004 (t0) REVERT: N 55 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7190 (mt-10) REVERT: N 60 MET cc_start: 0.5697 (mmp) cc_final: 0.5413 (mmm) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.1768 time to fit residues: 23.1312 Evaluate side-chains 88 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4029 Z= 0.237 Angle : 0.763 12.787 5485 Z= 0.385 Chirality : 0.046 0.175 603 Planarity : 0.005 0.036 703 Dihedral : 6.737 41.569 541 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.12 % Favored : 89.68 % Rotamer: Outliers : 4.40 % Allowed : 17.59 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.34), residues: 494 helix: None (None), residues: 0 sheet: -1.10 (0.37), residues: 178 loop : -2.72 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP N 112 HIS 0.004 0.002 HIS B 49 PHE 0.027 0.003 PHE B 135 TYR 0.020 0.002 TYR N 61 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 PHE cc_start: 0.8043 (m-10) cc_final: 0.7534 (m-10) REVERT: B 79 PHE cc_start: 0.6609 (m-80) cc_final: 0.6275 (m-80) REVERT: B 116 SER cc_start: 0.7496 (m) cc_final: 0.7122 (p) REVERT: B 129 LYS cc_start: 0.7695 (mttt) cc_final: 0.7310 (ttmt) REVERT: B 177 MET cc_start: 0.5569 (ppp) cc_final: 0.4813 (mtp) REVERT: B 178 ASP cc_start: 0.6252 (t0) cc_final: 0.6021 (t0) REVERT: B 224 GLU cc_start: 0.8071 (pm20) cc_final: 0.7584 (pm20) REVERT: N 53 ASP cc_start: 0.8422 (t0) cc_final: 0.8134 (t0) REVERT: N 55 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7143 (mt-10) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.1775 time to fit residues: 23.6864 Evaluate side-chains 98 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 114 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 245 HIS ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4029 Z= 0.245 Angle : 0.778 14.875 5485 Z= 0.382 Chirality : 0.045 0.180 603 Planarity : 0.005 0.051 703 Dihedral : 6.231 34.002 541 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.72 % Favored : 90.08 % Rotamer: Outliers : 6.02 % Allowed : 17.82 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -2.75 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.85 (0.39), residues: 172 loop : -2.55 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP G 36 HIS 0.010 0.002 HIS B 69 PHE 0.023 0.003 PHE N 109 TYR 0.024 0.002 TYR G 37 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6513 (m-80) cc_final: 0.6158 (m-80) REVERT: B 115 GLN cc_start: 0.8122 (mm110) cc_final: 0.7906 (tp-100) REVERT: B 116 SER cc_start: 0.7385 (m) cc_final: 0.6801 (p) REVERT: B 129 LYS cc_start: 0.7689 (mttt) cc_final: 0.7440 (ttmt) REVERT: B 168 PHE cc_start: 0.7207 (t80) cc_final: 0.6837 (t80) REVERT: B 177 MET cc_start: 0.5760 (ppp) cc_final: 0.4979 (mtp) REVERT: B 178 ASP cc_start: 0.6086 (t0) cc_final: 0.5807 (t0) REVERT: B 224 GLU cc_start: 0.8108 (pm20) cc_final: 0.7534 (pm20) REVERT: G 48 LEU cc_start: 0.7086 (mp) cc_final: 0.6786 (mt) REVERT: N 37 TRP cc_start: 0.8319 (m100) cc_final: 0.7996 (m100) REVERT: N 55 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7245 (mt-10) REVERT: N 82 MET cc_start: 0.7562 (tmm) cc_final: 0.6837 (tmm) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.1528 time to fit residues: 21.4235 Evaluate side-chains 110 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN G 31 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4029 Z= 0.247 Angle : 0.759 10.448 5485 Z= 0.376 Chirality : 0.045 0.161 603 Planarity : 0.005 0.039 703 Dihedral : 6.053 29.352 541 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.73 % Favored : 89.07 % Rotamer: Outliers : 5.32 % Allowed : 20.37 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.62 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.70 (0.39), residues: 175 loop : -2.51 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP N 112 HIS 0.003 0.001 HIS B 49 PHE 0.018 0.002 PHE N 109 TYR 0.032 0.002 TYR G 37 ARG 0.008 0.001 ARG N 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 GLN cc_start: 0.8016 (mm110) cc_final: 0.7785 (tp-100) REVERT: B 116 SER cc_start: 0.7200 (m) cc_final: 0.6898 (m) REVERT: B 129 LYS cc_start: 0.7706 (mttt) cc_final: 0.7382 (ttmt) REVERT: B 177 MET cc_start: 0.5795 (ppp) cc_final: 0.5006 (mtp) REVERT: B 178 ASP cc_start: 0.5924 (t0) cc_final: 0.5655 (t0) REVERT: B 224 GLU cc_start: 0.8182 (pm20) cc_final: 0.7576 (pm20) REVERT: G 48 LEU cc_start: 0.6981 (mp) cc_final: 0.6752 (mt) REVERT: N 35 MET cc_start: 0.7859 (mmp) cc_final: 0.7557 (mmm) REVERT: N 55 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7429 (mt-10) REVERT: N 82 MET cc_start: 0.7412 (tmm) cc_final: 0.6679 (tmm) outliers start: 23 outliers final: 20 residues processed: 112 average time/residue: 0.1584 time to fit residues: 22.0841 Evaluate side-chains 106 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4029 Z= 0.265 Angle : 0.757 10.622 5485 Z= 0.377 Chirality : 0.046 0.246 603 Planarity : 0.007 0.120 703 Dihedral : 6.171 30.594 541 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.73 % Favored : 89.07 % Rotamer: Outliers : 6.48 % Allowed : 20.37 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.52 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.45 (0.40), residues: 173 loop : -2.55 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP N 112 HIS 0.004 0.001 HIS B 49 PHE 0.030 0.002 PHE N 109 TYR 0.018 0.002 TYR B 248 ARG 0.018 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6637 (m-80) cc_final: 0.6151 (m-80) REVERT: B 116 SER cc_start: 0.7167 (m) cc_final: 0.6839 (m) REVERT: B 177 MET cc_start: 0.5904 (ppp) cc_final: 0.5079 (mtp) REVERT: B 178 ASP cc_start: 0.6046 (t0) cc_final: 0.5777 (t0) REVERT: B 224 GLU cc_start: 0.8195 (pm20) cc_final: 0.7565 (pm20) REVERT: G 48 LEU cc_start: 0.7099 (mp) cc_final: 0.6831 (mt) REVERT: G 99 VAL cc_start: 0.6795 (t) cc_final: 0.6482 (t) REVERT: N 55 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7693 (mt-10) REVERT: N 96 TYR cc_start: 0.7867 (m-80) cc_final: 0.7296 (m-10) outliers start: 28 outliers final: 25 residues processed: 112 average time/residue: 0.1418 time to fit residues: 20.0988 Evaluate side-chains 112 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Chi-restraints excluded: chain N residue 109 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 239 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.7737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4029 Z= 0.224 Angle : 0.751 9.315 5485 Z= 0.378 Chirality : 0.045 0.168 603 Planarity : 0.005 0.045 703 Dihedral : 6.085 26.834 541 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.34 % Favored : 88.46 % Rotamer: Outliers : 6.71 % Allowed : 21.76 % Favored : 71.53 % 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: -2.43 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.34 (0.38), residues: 181 loop : -2.58 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP N 112 HIS 0.005 0.002 HIS B 69 PHE 0.021 0.002 PHE B 275 TYR 0.018 0.002 TYR G 88 ARG 0.004 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6624 (mm110) cc_final: 0.5649 (pt0) REVERT: B 79 PHE cc_start: 0.6562 (m-80) cc_final: 0.6043 (m-80) REVERT: B 116 SER cc_start: 0.7153 (m) cc_final: 0.6519 (p) REVERT: B 177 MET cc_start: 0.5813 (ppp) cc_final: 0.5018 (mtp) REVERT: B 178 ASP cc_start: 0.6034 (t0) cc_final: 0.5817 (t0) REVERT: B 224 GLU cc_start: 0.8116 (pm20) cc_final: 0.7459 (pm20) REVERT: G 48 LEU cc_start: 0.7043 (mp) cc_final: 0.6795 (mt) REVERT: N 55 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7839 (mt-10) REVERT: N 82 MET cc_start: 0.7646 (tmm) cc_final: 0.7383 (tmm) REVERT: N 96 TYR cc_start: 0.7757 (m-80) cc_final: 0.7279 (m-10) outliers start: 29 outliers final: 24 residues processed: 106 average time/residue: 0.1322 time to fit residues: 18.0140 Evaluate side-chains 110 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Chi-restraints excluded: chain N residue 109 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4029 Z= 0.237 Angle : 0.737 9.717 5485 Z= 0.372 Chirality : 0.045 0.160 603 Planarity : 0.005 0.044 703 Dihedral : 5.993 25.741 541 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.74 % Favored : 88.06 % Rotamer: Outliers : 6.48 % Allowed : 22.69 % Favored : 70.83 % 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: -2.36 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.46 (0.39), residues: 177 loop : -2.38 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP N 112 HIS 0.003 0.001 HIS B 49 PHE 0.027 0.002 PHE B 58 TYR 0.021 0.002 TYR G 88 ARG 0.003 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6759 (mm110) cc_final: 0.5741 (pt0) REVERT: B 116 SER cc_start: 0.7371 (m) cc_final: 0.6657 (p) REVERT: B 177 MET cc_start: 0.5761 (ppp) cc_final: 0.5050 (mtp) REVERT: B 178 ASP cc_start: 0.6213 (t0) cc_final: 0.5921 (t0) REVERT: B 224 GLU cc_start: 0.8128 (pm20) cc_final: 0.7433 (pm20) REVERT: N 82 MET cc_start: 0.7583 (tmm) cc_final: 0.7252 (tmm) REVERT: N 96 TYR cc_start: 0.7820 (m-80) cc_final: 0.7312 (m-10) outliers start: 28 outliers final: 22 residues processed: 105 average time/residue: 0.1464 time to fit residues: 19.4018 Evaluate side-chains 105 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN G 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.8306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4029 Z= 0.202 Angle : 0.733 8.510 5485 Z= 0.367 Chirality : 0.046 0.147 603 Planarity : 0.005 0.044 703 Dihedral : 5.834 26.566 541 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.15 % Favored : 87.65 % Rotamer: Outliers : 5.32 % Allowed : 23.61 % Favored : 71.06 % 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: -2.21 (0.37), residues: 494 helix: None (None), residues: 0 sheet: -0.30 (0.39), residues: 187 loop : -2.37 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP N 112 HIS 0.003 0.001 HIS B 49 PHE 0.030 0.002 PHE B 58 TYR 0.021 0.002 TYR G 88 ARG 0.003 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6654 (mm110) cc_final: 0.5726 (pt0) REVERT: B 116 SER cc_start: 0.7444 (m) cc_final: 0.6733 (p) REVERT: B 177 MET cc_start: 0.5716 (ppp) cc_final: 0.5072 (mtt) REVERT: B 224 GLU cc_start: 0.8156 (pm20) cc_final: 0.7445 (pm20) REVERT: N 37 TRP cc_start: 0.8287 (m100) cc_final: 0.7958 (m100) REVERT: N 82 MET cc_start: 0.7546 (tmm) cc_final: 0.7253 (tmm) REVERT: N 96 TYR cc_start: 0.7766 (m-80) cc_final: 0.7325 (m-10) outliers start: 23 outliers final: 19 residues processed: 106 average time/residue: 0.1750 time to fit residues: 24.1234 Evaluate side-chains 105 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.0000 chunk 16 optimal weight: 0.0070 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN G 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4029 Z= 0.204 Angle : 0.736 8.589 5485 Z= 0.370 Chirality : 0.045 0.173 603 Planarity : 0.005 0.045 703 Dihedral : 5.776 29.493 541 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.15 % Favored : 87.65 % Rotamer: Outliers : 4.63 % Allowed : 25.00 % Favored : 70.37 % 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: -2.13 (0.37), residues: 494 helix: None (None), residues: 0 sheet: -0.18 (0.40), residues: 185 loop : -2.35 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP G 36 HIS 0.003 0.001 HIS B 49 PHE 0.025 0.002 PHE N 109 TYR 0.021 0.002 TYR G 88 ARG 0.004 0.001 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6532 (mm110) cc_final: 0.5652 (pt0) REVERT: B 116 SER cc_start: 0.7522 (m) cc_final: 0.6794 (p) REVERT: B 177 MET cc_start: 0.5757 (ppp) cc_final: 0.5267 (mtt) REVERT: B 224 GLU cc_start: 0.8135 (pm20) cc_final: 0.7423 (pm20) REVERT: N 37 TRP cc_start: 0.8235 (m100) cc_final: 0.7851 (m100) REVERT: N 82 MET cc_start: 0.7486 (tmm) cc_final: 0.7259 (tmm) REVERT: N 96 TYR cc_start: 0.7761 (m-80) cc_final: 0.7269 (m-10) outliers start: 20 outliers final: 18 residues processed: 102 average time/residue: 0.1354 time to fit residues: 17.6544 Evaluate side-chains 107 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 107 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** G 32 ASN ** 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 = 0.4504 r_free = 0.4504 target = 0.202104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133394 restraints weight = 4132.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.132258 restraints weight = 3579.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133542 restraints weight = 3125.113| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4029 Z= 0.210 Angle : 0.741 8.320 5485 Z= 0.373 Chirality : 0.045 0.172 603 Planarity : 0.005 0.049 703 Dihedral : 5.770 30.985 541 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.35 % Favored : 87.45 % Rotamer: Outliers : 4.63 % Allowed : 26.39 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.13 (0.37), residues: 494 helix: None (None), residues: 0 sheet: -0.25 (0.40), residues: 184 loop : -2.30 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP G 36 HIS 0.002 0.001 HIS B 49 PHE 0.024 0.002 PHE N 109 TYR 0.024 0.002 TYR G 88 ARG 0.003 0.001 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.49 seconds wall clock time: 26 minutes 57.27 seconds (1617.27 seconds total)