Starting phenix.real_space_refine on Mon Sep 23 16:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/09_2024/7d4g_30573.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/09_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_30573/09_2024/7d4g_30573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/09_2024/7d4g_30573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/09_2024/7d4g_30573.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/09_2024/7d4g_30573.cif" } 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. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.68, per 1000 atoms: 0.94 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 - 3.00 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: 0.82 Conformation dependent library (CDL) restraints added in 748.2 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: 0.44 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: 0.99 Time building geometry restraints manager: 0.99 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: 0.00 - 3.61: 5426 3.61 - 7.22: 52 7.22 - 10.83: 6 10.83 - 14.45: 0 14.45 - 18.06: 1 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 3.040 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 3.120 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 Time spend for trying shortcut: 0.00 ========== 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: 1.430 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- 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 : 0.404 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: 0.1862 time to fit residues: 32.7094 Evaluate side-chains 95 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4029 Z= 0.249 Angle : 0.836 11.545 5485 Z= 0.432 Chirality : 0.048 0.229 603 Planarity : 0.005 0.042 703 Dihedral : 7.412 45.207 541 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.89 % Rotamer: Outliers : 3.70 % Allowed : 13.66 % 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: -3.28 (0.31), residues: 494 helix: None (None), residues: 0 sheet: -1.22 (0.37), residues: 143 loop : -2.81 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP N 112 HIS 0.005 0.002 HIS B 49 PHE 0.030 0.003 PHE B 106 TYR 0.024 0.002 TYR G 88 ARG 0.004 0.001 ARG B 44 *********************** 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 112 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6648 (mm-40) cc_final: 0.6375 (mm110) REVERT: B 129 LYS cc_start: 0.7663 (mttt) cc_final: 0.7448 (ttmt) REVERT: B 168 PHE cc_start: 0.6548 (t80) cc_final: 0.6210 (t80) REVERT: B 177 MET cc_start: 0.5555 (ppp) cc_final: 0.4818 (mtp) REVERT: B 214 ARG cc_start: 0.6576 (mtp-110) cc_final: 0.6161 (ptm-80) REVERT: N 55 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7240 (mt-10) REVERT: N 60 MET cc_start: 0.6114 (mmp) cc_final: 0.5746 (mmm) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.1723 time to fit residues: 21.9714 Evaluate side-chains 88 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 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 G residue 3 VAL 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 105 THR 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4029 Z= 0.352 Angle : 0.823 13.400 5485 Z= 0.420 Chirality : 0.047 0.197 603 Planarity : 0.005 0.047 703 Dihedral : 7.063 40.882 541 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.92 % Favored : 89.88 % Rotamer: Outliers : 4.86 % Allowed : 17.36 % Favored : 77.78 % Cbeta Deviations : 0.00 % 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: -3.14 (0.34), residues: 494 helix: None (None), residues: 0 sheet: -1.37 (0.35), residues: 184 loop : -2.68 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP N 112 HIS 0.006 0.002 HIS B 207 PHE 0.026 0.003 PHE B 135 TYR 0.027 0.003 TYR B 248 ARG 0.008 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 120 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 SER cc_start: 0.7524 (m) cc_final: 0.7196 (p) REVERT: B 177 MET cc_start: 0.5884 (ppp) cc_final: 0.5086 (mtp) REVERT: B 178 ASP cc_start: 0.6239 (t0) cc_final: 0.5829 (t0) REVERT: B 224 GLU cc_start: 0.8163 (pm20) cc_final: 0.7582 (pm20) REVERT: N 39 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7568 (mtp180) REVERT: N 55 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7356 (mt-10) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.1776 time to fit residues: 23.7808 Evaluate side-chains 97 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 108 THR Chi-restraints excluded: chain B residue 120 VAL 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 G residue 3 VAL Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 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: 0.5548 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4029 Z= 0.224 Angle : 0.766 14.136 5485 Z= 0.382 Chirality : 0.046 0.200 603 Planarity : 0.005 0.046 703 Dihedral : 6.495 31.370 541 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.12 % Favored : 89.68 % Rotamer: Outliers : 5.79 % Allowed : 17.13 % Favored : 77.08 % 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: -2.72 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.67 (0.37), residues: 179 loop : -2.66 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP G 92 HIS 0.002 0.001 HIS B 49 PHE 0.023 0.002 PHE B 79 TYR 0.028 0.002 TYR G 37 ARG 0.007 0.001 ARG G 55 *********************** 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 119 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 LEU cc_start: 0.8020 (pt) cc_final: 0.7810 (pt) REVERT: B 79 PHE cc_start: 0.6776 (m-80) cc_final: 0.5604 (m-80) REVERT: B 116 SER cc_start: 0.7376 (m) cc_final: 0.6899 (p) REVERT: B 168 PHE cc_start: 0.7034 (t80) cc_final: 0.6678 (t80) REVERT: B 177 MET cc_start: 0.5976 (ppp) cc_final: 0.5139 (mtp) REVERT: B 224 GLU cc_start: 0.8169 (pm20) cc_final: 0.7504 (pm20) REVERT: N 53 ASP cc_start: 0.8370 (t0) cc_final: 0.8147 (t0) REVERT: N 55 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7600 (mt-10) REVERT: N 60 MET cc_start: 0.7969 (mmm) cc_final: 0.7481 (mmm) REVERT: N 71 MET cc_start: 0.8962 (ppp) cc_final: 0.8727 (ppp) outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 0.1578 time to fit residues: 21.2866 Evaluate side-chains 102 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 120 VAL 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 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 96 LEU Chi-restraints excluded: chain N residue 2 VAL 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: 2.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** G 32 ASN N 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4029 Z= 0.285 Angle : 0.778 11.983 5485 Z= 0.388 Chirality : 0.046 0.176 603 Planarity : 0.006 0.053 703 Dihedral : 6.420 27.956 541 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.93 % Favored : 88.87 % Rotamer: Outliers : 7.18 % Allowed : 18.06 % Favored : 74.77 % 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: -2.65 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.61 (0.39), residues: 172 loop : -2.60 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP N 112 HIS 0.013 0.003 HIS B 69 PHE 0.016 0.002 PHE B 135 TYR 0.024 0.002 TYR B 248 ARG 0.008 0.001 ARG B 78 *********************** 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 122 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: B 80 ASP cc_start: 0.7150 (t0) cc_final: 0.6799 (t0) REVERT: B 116 SER cc_start: 0.7290 (m) cc_final: 0.6883 (p) REVERT: B 177 MET cc_start: 0.5964 (ppp) cc_final: 0.5245 (mtp) REVERT: B 224 GLU cc_start: 0.8214 (pm20) cc_final: 0.7550 (pm20) REVERT: N 53 ASP cc_start: 0.8415 (t0) cc_final: 0.8167 (t0) REVERT: N 55 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7624 (mt-10) REVERT: N 60 MET cc_start: 0.8041 (mmm) cc_final: 0.7776 (mmm) REVERT: N 96 TYR cc_start: 0.7750 (m-80) cc_final: 0.7266 (m-10) outliers start: 31 outliers final: 25 residues processed: 107 average time/residue: 0.1513 time to fit residues: 20.2037 Evaluate side-chains 105 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 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 79 PHE 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 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 32 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 VAL 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: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.7651 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= 0.219 Angle : 0.757 10.602 5485 Z= 0.378 Chirality : 0.046 0.162 603 Planarity : 0.005 0.039 703 Dihedral : 6.116 27.081 541 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.93 % Favored : 88.87 % Rotamer: Outliers : 6.25 % Allowed : 19.91 % Favored : 73.84 % 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: -2.60 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.70 (0.39), residues: 175 loop : -2.48 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP N 112 HIS 0.003 0.001 HIS B 207 PHE 0.015 0.002 PHE B 135 TYR 0.023 0.002 TYR G 37 ARG 0.005 0.001 ARG G 55 *********************** 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 118 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: B 116 SER cc_start: 0.7242 (m) cc_final: 0.6656 (p) REVERT: B 145 TYR cc_start: 0.7081 (t80) cc_final: 0.6478 (t80) REVERT: B 168 PHE cc_start: 0.7045 (t80) cc_final: 0.6722 (t80) REVERT: B 177 MET cc_start: 0.5983 (ppp) cc_final: 0.5305 (mtt) REVERT: B 221 SER cc_start: 0.7601 (m) cc_final: 0.7395 (m) REVERT: B 224 GLU cc_start: 0.8186 (pm20) cc_final: 0.7481 (pm20) REVERT: G 48 LEU cc_start: 0.7164 (mp) cc_final: 0.6878 (mt) REVERT: N 37 TRP cc_start: 0.8235 (m100) cc_final: 0.7869 (m100) REVERT: N 53 ASP cc_start: 0.8415 (t0) cc_final: 0.8125 (t0) REVERT: N 55 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7853 (mt-10) REVERT: N 82 MET cc_start: 0.7571 (tmm) cc_final: 0.7230 (tmm) REVERT: N 96 TYR cc_start: 0.7871 (m-80) cc_final: 0.7462 (m-10) outliers start: 27 outliers final: 24 residues processed: 106 average time/residue: 0.1344 time to fit residues: 18.2345 Evaluate side-chains 109 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 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 79 PHE 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 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 17 LYS Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** G 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.7930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4029 Z= 0.237 Angle : 0.767 10.590 5485 Z= 0.387 Chirality : 0.045 0.158 603 Planarity : 0.005 0.045 703 Dihedral : 6.041 26.253 541 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.94 % Favored : 87.85 % Rotamer: Outliers : 6.02 % Allowed : 21.53 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.63 (0.38), residues: 190 loop : -2.46 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP N 112 HIS 0.003 0.001 HIS B 207 PHE 0.021 0.002 PHE N 109 TYR 0.018 0.002 TYR B 248 ARG 0.008 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 121 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6422 (mm-40) cc_final: 0.5415 (pt0) REVERT: B 79 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: B 150 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6765 (tptp) REVERT: B 177 MET cc_start: 0.6010 (ppp) cc_final: 0.5342 (mtt) REVERT: B 224 GLU cc_start: 0.8198 (pm20) cc_final: 0.7482 (pm20) REVERT: G 48 LEU cc_start: 0.7274 (mp) cc_final: 0.7033 (mt) REVERT: N 37 TRP cc_start: 0.8302 (m100) cc_final: 0.7882 (m100) REVERT: N 53 ASP cc_start: 0.8470 (t0) cc_final: 0.8199 (t0) REVERT: N 55 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7901 (mt-10) REVERT: N 82 MET cc_start: 0.7550 (tmm) cc_final: 0.7249 (tmm) REVERT: N 96 TYR cc_start: 0.7613 (m-80) cc_final: 0.7354 (m-10) outliers start: 26 outliers final: 25 residues processed: 108 average time/residue: 0.1316 time to fit residues: 18.1662 Evaluate side-chains 111 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 79 PHE 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 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 17 LYS Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 VAL 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: 0.0670 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 164 ASN G 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.8216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4029 Z= 0.220 Angle : 0.751 10.131 5485 Z= 0.377 Chirality : 0.046 0.159 603 Planarity : 0.005 0.043 703 Dihedral : 6.131 26.333 541 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.54 % Favored : 88.26 % Rotamer: Outliers : 5.09 % Allowed : 24.77 % Favored : 70.14 % 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: -2.32 (0.37), residues: 494 helix: None (None), residues: 0 sheet: -0.46 (0.39), residues: 187 loop : -2.38 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP N 112 HIS 0.002 0.001 HIS B 245 PHE 0.024 0.002 PHE B 133 TYR 0.014 0.002 TYR B 248 ARG 0.007 0.001 ARG G 55 *********************** 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 113 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6354 (mm-40) cc_final: 0.5517 (pt0) REVERT: B 50 SER cc_start: 0.7450 (m) cc_final: 0.7137 (t) REVERT: B 79 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: B 116 SER cc_start: 0.7489 (m) cc_final: 0.6768 (p) REVERT: B 131 CYS cc_start: 0.5229 (t) cc_final: 0.4789 (t) REVERT: B 150 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6598 (tppp) REVERT: B 168 PHE cc_start: 0.7445 (t80) cc_final: 0.6849 (t80) REVERT: B 177 MET cc_start: 0.6003 (ppp) cc_final: 0.5353 (mtt) REVERT: B 224 GLU cc_start: 0.8177 (pm20) cc_final: 0.7451 (pm20) REVERT: N 37 TRP cc_start: 0.8188 (m100) cc_final: 0.7878 (m100) REVERT: N 53 ASP cc_start: 0.8513 (t0) cc_final: 0.8290 (t0) REVERT: N 55 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8026 (mt-10) REVERT: N 82 MET cc_start: 0.7525 (tmm) cc_final: 0.7198 (tmm) REVERT: N 96 TYR cc_start: 0.7613 (m-80) cc_final: 0.7388 (m-10) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.1217 time to fit residues: 16.4858 Evaluate side-chains 104 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain B residue 79 PHE 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 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 73 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 107 TYR Chi-restraints excluded: chain N residue 109 PHE 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: 0.3980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.8478 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= 0.227 Angle : 0.745 9.955 5485 Z= 0.374 Chirality : 0.046 0.152 603 Planarity : 0.005 0.048 703 Dihedral : 6.031 26.360 541 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.75 % Favored : 87.04 % Rotamer: Outliers : 5.09 % Allowed : 24.54 % 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: -2.12 (0.38), residues: 494 helix: None (None), residues: 0 sheet: -0.30 (0.39), residues: 185 loop : -2.25 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP N 112 HIS 0.003 0.001 HIS B 245 PHE 0.019 0.002 PHE N 109 TYR 0.014 0.002 TYR B 248 ARG 0.005 0.001 ARG G 55 *********************** 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 111 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6389 (mm-40) cc_final: 0.5554 (pt0) REVERT: B 50 SER cc_start: 0.7499 (m) cc_final: 0.7209 (t) REVERT: B 79 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: B 145 TYR cc_start: 0.7568 (t80) cc_final: 0.7344 (t80) REVERT: B 150 LYS cc_start: 0.7482 (mmmt) cc_final: 0.6689 (tppp) REVERT: B 177 MET cc_start: 0.5975 (ppp) cc_final: 0.5452 (mtt) REVERT: B 224 GLU cc_start: 0.8126 (pm20) cc_final: 0.7423 (pm20) REVERT: N 37 TRP cc_start: 0.8193 (m100) cc_final: 0.7912 (m100) REVERT: N 53 ASP cc_start: 0.8466 (t0) cc_final: 0.8230 (t0) REVERT: N 55 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8078 (mt-10) outliers start: 22 outliers final: 18 residues processed: 103 average time/residue: 0.1394 time to fit residues: 18.4378 Evaluate side-chains 101 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 79 PHE 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 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 35 SER Chi-restraints excluded: chain G residue 48 LEU 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 69 VAL 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: 0.9990 chunk 23 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS G 32 ASN N 7 GLN N 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.8725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4029 Z= 0.236 Angle : 0.794 14.410 5485 Z= 0.389 Chirality : 0.047 0.171 603 Planarity : 0.005 0.046 703 Dihedral : 6.123 27.431 541 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.35 % Favored : 87.45 % Rotamer: Outliers : 5.09 % Allowed : 25.23 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.38), residues: 494 helix: None (None), residues: 0 sheet: -0.20 (0.40), residues: 182 loop : -2.23 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G 36 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.002 PHE B 168 TYR 0.015 0.002 TYR B 248 ARG 0.002 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 109 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.6500 (mm-40) cc_final: 0.5490 (pt0) REVERT: B 50 SER cc_start: 0.7520 (m) cc_final: 0.7242 (t) REVERT: B 79 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6217 (m-80) REVERT: B 116 SER cc_start: 0.7427 (m) cc_final: 0.6924 (p) REVERT: B 131 CYS cc_start: 0.5286 (t) cc_final: 0.4735 (t) REVERT: B 145 TYR cc_start: 0.7603 (t80) cc_final: 0.7403 (t80) REVERT: B 150 LYS cc_start: 0.7561 (mmmt) cc_final: 0.6931 (tptp) REVERT: B 168 PHE cc_start: 0.7390 (t80) cc_final: 0.6800 (t80) REVERT: B 177 MET cc_start: 0.5969 (ppp) cc_final: 0.5475 (mtt) REVERT: B 224 GLU cc_start: 0.8105 (pm20) cc_final: 0.7313 (pm20) REVERT: N 7 GLN cc_start: 0.3021 (OUTLIER) cc_final: 0.2325 (mt0) REVERT: N 37 TRP cc_start: 0.8231 (m100) cc_final: 0.7991 (m100) REVERT: N 53 ASP cc_start: 0.8470 (t0) cc_final: 0.8218 (t0) REVERT: N 55 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8100 (mt-10) outliers start: 22 outliers final: 19 residues processed: 99 average time/residue: 0.1207 time to fit residues: 16.4096 Evaluate side-chains 104 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 79 PHE 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 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 31 ASN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 48 LEU 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 7 GLN Chi-restraints excluded: chain N residue 69 VAL 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: 0.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.204256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.134854 restraints weight = 4451.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.138468 restraints weight = 3335.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.141635 restraints weight = 2754.437| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.8943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4029 Z= 0.212 Angle : 0.782 13.695 5485 Z= 0.388 Chirality : 0.047 0.182 603 Planarity : 0.005 0.049 703 Dihedral : 6.069 29.658 541 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.55 % Favored : 87.25 % Rotamer: Outliers : 5.32 % Allowed : 25.46 % Favored : 69.21 % 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: -2.01 (0.38), residues: 494 helix: None (None), residues: 0 sheet: -0.21 (0.39), residues: 188 loop : -2.20 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP G 36 HIS 0.004 0.001 HIS B 69 PHE 0.020 0.002 PHE B 168 TYR 0.011 0.002 TYR G 37 ARG 0.003 0.001 ARG G 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.55 seconds wall clock time: 30 minutes 1.25 seconds (1801.25 seconds total)