Starting phenix.real_space_refine (version: dev) on Tue Nov 29 14:00:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/11_2022/7f73_31484.pdb" } resolution = 4.0 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= 0.007 sd= 0.086 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2467 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2467 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Time building chain proxies: 3.19, per 1000 atoms: 0.65 Number of scatterers: 4934 At special positions: 0 Unit cell: (83.699, 118.483, 94.569, 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 22 16.00 O 848 8.00 N 816 7.00 C 3248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.02 Conformation dependent library (CDL) restraints added in 670.6 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 64 Processing helix chain 'A' and resid 69 through 97 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.338A pdb=" N ALA A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.724A pdb=" N ASP A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.608A pdb=" N SER A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 235 removed outlier: 3.549A pdb=" N GLN A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 296 removed outlier: 3.948A pdb=" N SER A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 329 removed outlier: 3.567A pdb=" N PHE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 64 Processing helix chain 'B' and resid 69 through 97 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.338A pdb=" N ALA B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 182 removed outlier: 3.724A pdb=" N ASP B 157 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 205 removed outlier: 4.608A pdb=" N SER B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 235 removed outlier: 3.549A pdb=" N GLN B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN B 217 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 296 removed outlier: 3.948A pdb=" N SER B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 329 removed outlier: 3.566A pdb=" N PHE B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1233 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: 1.31 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1078 1.33 - 1.45: 1216 1.45 - 1.57: 2742 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 5064 Sorted by residual: bond pdb=" N THR B 205 " pdb=" CA THR B 205 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.10e-02 8.26e+03 1.11e+01 bond pdb=" N THR A 205 " pdb=" CA THR A 205 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.10e-02 8.26e+03 1.10e+01 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.05e+00 bond pdb=" N VAL B 202 " pdb=" CA VAL B 202 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N PHE A 149 " pdb=" CA PHE A 149 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.27e-02 6.20e+03 8.22e+00 ... (remaining 5059 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.93: 94 106.93 - 113.76: 2723 113.76 - 120.58: 2329 120.58 - 127.41: 1644 127.41 - 134.24: 54 Bond angle restraints: 6844 Sorted by residual: angle pdb=" C PHE A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 122.97 117.47 5.50 9.80e-01 1.04e+00 3.14e+01 angle pdb=" C PHE B 149 " pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 122.97 117.51 5.46 9.80e-01 1.04e+00 3.11e+01 angle pdb=" CA GLN B 78 " pdb=" CB GLN B 78 " pdb=" CG GLN B 78 " ideal model delta sigma weight residual 114.10 124.10 -10.00 2.00e+00 2.50e-01 2.50e+01 angle pdb=" CA GLN A 78 " pdb=" CB GLN A 78 " pdb=" CG GLN A 78 " ideal model delta sigma weight residual 114.10 124.09 -9.99 2.00e+00 2.50e-01 2.49e+01 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 113.41 118.88 -5.47 1.22e+00 6.72e-01 2.01e+01 ... (remaining 6839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 2566 17.01 - 34.02: 300 34.02 - 51.03: 68 51.03 - 68.04: 15 68.04 - 85.05: 3 Dihedral angle restraints: 2952 sinusoidal: 1208 harmonic: 1744 Sorted by residual: dihedral pdb=" CA TRP B 188 " pdb=" C TRP B 188 " pdb=" N TRP B 189 " pdb=" CA TRP B 189 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TRP A 188 " pdb=" C TRP A 188 " pdb=" N TRP A 189 " pdb=" CA TRP A 189 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG B 299 " pdb=" C ARG B 299 " pdb=" N GLU B 300 " pdb=" CA GLU B 300 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.79e+00 ... (remaining 2949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 516 0.049 - 0.099: 147 0.099 - 0.148: 55 0.148 - 0.197: 25 0.197 - 0.246: 5 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA MET A 203 " pdb=" N MET A 203 " pdb=" C MET A 203 " pdb=" CB MET A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA MET B 203 " pdb=" N MET B 203 " pdb=" C MET B 203 " pdb=" CB MET B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA TYR A 96 " pdb=" N TYR A 96 " pdb=" C TYR A 96 " pdb=" CB TYR A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 745 not shown) Planarity restraints: 844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 206 " -0.008 2.00e-02 2.50e+03 1.31e-02 4.31e+00 pdb=" CG TRP B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 206 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 206 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 206 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 206 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.008 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 206 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 90 " 0.010 2.00e-02 2.50e+03 1.49e-02 3.89e+00 pdb=" CG PHE B 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 90 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 90 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 90 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 90 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 90 " -0.001 2.00e-02 2.50e+03 ... (remaining 841 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1010 2.78 - 3.31: 5029 3.31 - 3.84: 7936 3.84 - 4.37: 8858 4.37 - 4.90: 14744 Nonbonded interactions: 37577 Sorted by model distance: nonbonded pdb=" OE1 GLN A 230 " pdb=" OE1 GLN A 233 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLN B 230 " pdb=" OE1 GLN B 233 " model vdw 2.247 3.040 nonbonded pdb=" NE ARG A 86 " pdb=" CZ PHE A 90 " model vdw 2.290 3.420 nonbonded pdb=" NE ARG B 86 " pdb=" CZ PHE B 90 " model vdw 2.290 3.420 nonbonded pdb=" O LYS A 49 " pdb=" ND1 HIS A 53 " model vdw 2.303 2.520 ... (remaining 37572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3248 2.51 5 N 816 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 2.590 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.007 0.045 5064 Z= 0.415 Angle : 1.070 10.003 6844 Z= 0.679 Chirality : 0.061 0.246 748 Planarity : 0.005 0.027 844 Dihedral : 15.265 85.051 1820 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.32), residues: 578 helix: 0.32 (0.22), residues: 476 sheet: None (None), residues: 0 loop : -0.25 (0.51), residues: 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 121 average time/residue: 0.1868 time to fit residues: 27.9979 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0501 time to fit residues: 1.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN A 302 GLN B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5064 Z= 0.182 Angle : 0.637 10.057 6844 Z= 0.337 Chirality : 0.038 0.167 748 Planarity : 0.004 0.024 844 Dihedral : 4.609 17.202 638 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.24 % 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: 2.06 (0.33), residues: 578 helix: 1.81 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -0.67 (0.58), residues: 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.1680 time to fit residues: 18.7300 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0507 time to fit residues: 1.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS B 40 GLN B 50 GLN B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5064 Z= 0.204 Angle : 0.648 8.638 6844 Z= 0.342 Chirality : 0.038 0.150 748 Planarity : 0.004 0.026 844 Dihedral : 4.348 17.513 638 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.34), residues: 578 helix: 2.04 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -0.68 (0.61), residues: 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.605 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.1595 time to fit residues: 18.6104 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0503 time to fit residues: 1.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 5064 Z= 0.218 Angle : 0.671 10.786 6844 Z= 0.349 Chirality : 0.039 0.170 748 Planarity : 0.004 0.025 844 Dihedral : 4.312 17.224 638 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 3.92 % 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: 2.41 (0.34), residues: 578 helix: 1.96 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -0.59 (0.64), residues: 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.629 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 0.1491 time to fit residues: 18.0829 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0492 time to fit residues: 1.9709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 32 optimal weight: 10.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5064 Z= 0.219 Angle : 0.694 8.789 6844 Z= 0.362 Chirality : 0.041 0.185 748 Planarity : 0.004 0.029 844 Dihedral : 4.286 16.917 638 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.87 % 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: 2.24 (0.34), residues: 578 helix: 1.89 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.34 (0.62), residues: 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.543 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 0.1532 time to fit residues: 16.4870 Evaluate side-chains 75 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0467 time to fit residues: 1.1529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.0060 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5064 Z= 0.169 Angle : 0.651 10.473 6844 Z= 0.340 Chirality : 0.038 0.183 748 Planarity : 0.003 0.023 844 Dihedral : 4.154 16.333 638 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.87 % 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: 2.52 (0.34), residues: 578 helix: 2.10 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.34 (0.60), residues: 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.580 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.1415 time to fit residues: 14.7536 Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0580 time to fit residues: 1.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5064 Z= 0.165 Angle : 0.663 11.068 6844 Z= 0.349 Chirality : 0.040 0.238 748 Planarity : 0.003 0.027 844 Dihedral : 4.093 16.933 638 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.87 % 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 (0.34), residues: 578 helix: 2.15 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.27 (0.61), residues: 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.586 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.1367 time to fit residues: 14.2730 Evaluate side-chains 70 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0526 time to fit residues: 1.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5064 Z= 0.166 Angle : 0.675 14.203 6844 Z= 0.353 Chirality : 0.039 0.227 748 Planarity : 0.003 0.022 844 Dihedral : 4.080 17.299 638 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.34), residues: 578 helix: 2.17 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.1532 time to fit residues: 15.7496 Evaluate side-chains 69 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0523 time to fit residues: 1.1799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN B 78 GLN B 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5064 Z= 0.204 Angle : 0.741 13.742 6844 Z= 0.383 Chirality : 0.041 0.271 748 Planarity : 0.004 0.029 844 Dihedral : 4.085 19.204 638 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.68 % 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: 2.62 (0.34), residues: 578 helix: 2.17 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -1.27 (0.61), residues: 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.559 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.1405 time to fit residues: 13.8605 Evaluate side-chains 67 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0515 time to fit residues: 1.2561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5064 Z= 0.201 Angle : 0.779 18.834 6844 Z= 0.394 Chirality : 0.040 0.250 748 Planarity : 0.003 0.021 844 Dihedral : 4.106 17.798 638 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.19 % 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: 2.59 (0.34), residues: 578 helix: 2.16 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -1.37 (0.61), residues: 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.575 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.1535 time to fit residues: 13.8609 Evaluate side-chains 64 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0748 time to fit residues: 0.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169268 restraints weight = 7271.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.166692 restraints weight = 11668.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.164150 restraints weight = 11147.391| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.060 5064 Z= 0.520 Angle : 0.992 13.826 6844 Z= 0.525 Chirality : 0.051 0.219 748 Planarity : 0.005 0.038 844 Dihedral : 4.768 19.078 638 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.33), residues: 578 helix: 1.14 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 74 =============================================================================== Job complete usr+sys time: 1046.39 seconds wall clock time: 19 minutes 54.85 seconds (1194.85 seconds total)