Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 01:55:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/04_2023/7d4g_30573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/04_2023/7d4g_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_30573/04_2023/7d4g_30573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/04_2023/7d4g_30573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/04_2023/7d4g_30573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4g_30573/04_2023/7d4g_30573.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 1.45 Conformation dependent library (CDL) restraints added in 688.8 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: 0.27 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: 1.02 Time building geometry restraints manager: 1.61 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.880 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1840 time to fit residues: 32.2440 Evaluate side-chains 94 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6179 ------------------------------------------------------------------------------- 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: 0.0770 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: 0.4778 ------------------------------------------------------------------------------- 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 122 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN G 6 GLN G 31 ASN G 39 GLN G 80 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4029 Z= 0.234 Angle : 0.824 11.514 5485 Z= 0.421 Chirality : 0.047 0.210 603 Planarity : 0.005 0.041 703 Dihedral : 7.334 44.877 541 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.89 % Rotamer Outliers : 3.70 % 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: -1.27 (0.37), residues: 143 loop : -2.79 (0.27), residues: 351 *********************** 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 116 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.1905 time to fit residues: 24.6479 Evaluate side-chains 87 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0387 time to fit residues: 1.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4029 Z= 0.224 Angle : 0.778 16.428 5485 Z= 0.387 Chirality : 0.046 0.169 603 Planarity : 0.005 0.050 703 Dihedral : 6.678 41.636 541 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.92 % Favored : 89.88 % Rotamer Outliers : 3.47 % 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: -3.11 (0.34), residues: 494 helix: None (None), residues: 0 sheet: -1.30 (0.37), residues: 181 loop : -2.69 (0.31), residues: 313 *********************** 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 123 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.1533 time to fit residues: 22.1116 Evaluate side-chains 92 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0455 time to fit residues: 1.3349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- 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: 0.5435 moved from start: 0.6294 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= 0.195 Angle : 0.755 11.530 5485 Z= 0.374 Chirality : 0.045 0.175 603 Planarity : 0.005 0.032 703 Dihedral : 6.187 34.704 541 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.72 % Favored : 90.08 % Rotamer Outliers : 3.01 % 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: -2.80 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -1.10 (0.36), residues: 192 loop : -2.49 (0.33), residues: 302 *********************** 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 116 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1618 time to fit residues: 21.8429 Evaluate side-chains 95 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0438 time to fit residues: 1.3023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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** ** 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: 0.5556 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 4029 Z= 0.261 Angle : 0.749 9.338 5485 Z= 0.376 Chirality : 0.046 0.228 603 Planarity : 0.006 0.102 703 Dihedral : 6.008 29.361 541 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.73 % Favored : 89.07 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.84 (0.36), residues: 188 loop : -2.47 (0.33), residues: 306 *********************** 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 108 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.1594 time to fit residues: 20.4568 Evaluate side-chains 96 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0477 time to fit residues: 1.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.0870 chunk 34 optimal weight: 8.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 69 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: 0.5556 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4029 Z= 0.239 Angle : 0.746 11.669 5485 Z= 0.370 Chirality : 0.045 0.172 603 Planarity : 0.005 0.043 703 Dihedral : 5.973 29.991 541 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.53 % Favored : 89.27 % Rotamer Outliers : 2.08 % 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: -2.49 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.90 (0.35), residues: 201 loop : -2.30 (0.35), residues: 293 *********************** 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 101 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.1679 time to fit residues: 19.9851 Evaluate side-chains 87 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0437 time to fit residues: 1.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 4029 Z= 0.329 Angle : 0.795 9.882 5485 Z= 0.399 Chirality : 0.046 0.182 603 Planarity : 0.005 0.042 703 Dihedral : 6.139 27.290 541 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.94 % Favored : 87.85 % Rotamer Outliers : 2.78 % 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: -2.67 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.96 (0.38), residues: 171 loop : -2.38 (0.32), residues: 323 *********************** 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 95 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.1288 time to fit residues: 14.4199 Evaluate side-chains 87 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.432 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0447 time to fit residues: 1.3268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.5576 moved from start: 0.8226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4029 Z= 0.217 Angle : 0.766 9.102 5485 Z= 0.383 Chirality : 0.045 0.143 603 Planarity : 0.005 0.039 703 Dihedral : 5.999 26.019 541 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.74 % Favored : 88.06 % Rotamer Outliers : 2.08 % 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: -2.42 (0.35), residues: 494 helix: None (None), residues: 0 sheet: -0.48 (0.40), residues: 164 loop : -2.37 (0.31), residues: 330 *********************** 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 97 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.463 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 0.1435 time to fit residues: 16.7080 Evaluate side-chains 84 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0417 time to fit residues: 0.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 43 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.8613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 4029 Z= 0.296 Angle : 0.790 8.509 5485 Z= 0.398 Chirality : 0.047 0.206 603 Planarity : 0.005 0.040 703 Dihedral : 6.145 27.036 541 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.55 % Favored : 87.25 % Rotamer Outliers : 2.08 % 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: -2.51 (0.36), residues: 494 helix: None (None), residues: 0 sheet: -0.52 (0.40), residues: 168 loop : -2.47 (0.31), residues: 326 *********************** 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 94 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.417 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.1418 time to fit residues: 16.5760 Evaluate side-chains 81 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0445 time to fit residues: 1.0444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN G 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4029 Z= 0.218 Angle : 0.787 10.131 5485 Z= 0.394 Chirality : 0.046 0.180 603 Planarity : 0.005 0.051 703 Dihedral : 6.011 26.092 541 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.34 % Favored : 88.46 % Rotamer Outliers : 1.16 % 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: -2.20 (0.38), residues: 494 helix: None (None), residues: 0 sheet: -0.33 (0.39), residues: 197 loop : -2.39 (0.34), residues: 297 ********************** 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 95 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 91 average time/residue: 0.1487 time to fit residues: 17.3383 Evaluate side-chains 82 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0625 time to fit residues: 0.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.196856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.125461 restraints weight = 4242.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128655 restraints weight = 3315.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130536 restraints weight = 2787.776| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.9106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4029 Z= 0.233 Angle : 0.795 10.558 5485 Z= 0.400 Chirality : 0.046 0.176 603 Planarity : 0.005 0.047 703 Dihedral : 6.051 27.461 541 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.35 % Favored : 87.45 % Rotamer Outliers : 1.62 % 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: -2.19 (0.38), residues: 494 helix: None (None), residues: 0 sheet: -0.29 (0.40), residues: 194 loop : -2.40 (0.34), residues: 300 =============================================================================== Job complete usr+sys time: 1338.89 seconds wall clock time: 25 minutes 45.29 seconds (1545.29 seconds total)