Starting phenix.real_space_refine on Fri Aug 2 20:04:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/08_2024/7f73_31484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/08_2024/7f73_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_31484/08_2024/7f73_31484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/08_2024/7f73_31484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/08_2024/7f73_31484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/08_2024/7f73_31484.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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 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. 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-5409/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: 3.51, per 1000 atoms: 0.71 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: 1.95 Conformation dependent library (CDL) restraints added in 881.9 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: 0.46 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: 2.15 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 3.120 ... (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 Time spend for trying shortcut: 0.00 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 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: 0.810 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 % Allowed : 0.37 % Favored : 95.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 206 HIS 0.013 0.002 HIS B 192 PHE 0.034 0.002 PHE B 90 TYR 0.011 0.002 TYR A 125 ARG 0.003 0.001 ARG B 216 *********************** 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 : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7986 (t0) cc_final: 0.7583 (p0) REVERT: A 130 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: A 149 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: B 149 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4686 (m-80) outliers start: 22 outliers final: 8 residues processed: 121 average time/residue: 0.1993 time to fit residues: 29.6028 Evaluate side-chains 76 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 302 GLN B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5064 Z= 0.207 Angle : 0.643 7.231 6844 Z= 0.346 Chirality : 0.039 0.165 748 Planarity : 0.004 0.023 844 Dihedral : 8.489 57.460 659 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.10 % Allowed : 10.26 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.33), residues: 578 helix: 1.68 (0.23), residues: 478 sheet: None (None), residues: 0 loop : -0.63 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 206 HIS 0.005 0.001 HIS A 192 PHE 0.016 0.001 PHE B 290 TYR 0.013 0.002 TYR A 236 ARG 0.003 0.000 ARG B 27 *********************** 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 104 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8219 (t0) cc_final: 0.7503 (p0) REVERT: A 142 LEU cc_start: 0.7937 (tp) cc_final: 0.7715 (tp) REVERT: A 149 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5422 (m-80) REVERT: A 234 TYR cc_start: 0.7576 (t80) cc_final: 0.7266 (t80) REVERT: B 149 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: B 203 MET cc_start: 0.8027 (mmm) cc_final: 0.7654 (tpp) outliers start: 22 outliers final: 11 residues processed: 97 average time/residue: 0.1774 time to fit residues: 21.8396 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 302 GLN B 40 GLN B 50 GLN B 78 GLN B 192 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5064 Z= 0.210 Angle : 0.661 10.781 6844 Z= 0.350 Chirality : 0.039 0.158 748 Planarity : 0.004 0.024 844 Dihedral : 6.674 54.047 650 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.10 % Allowed : 16.23 % Favored : 79.66 % 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: 2.31 (0.34), residues: 578 helix: 1.94 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -0.61 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 12 HIS 0.008 0.001 HIS A 13 PHE 0.030 0.002 PHE A 91 TYR 0.020 0.001 TYR A 29 ARG 0.005 0.001 ARG B 63 *********************** 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 105 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8308 (t0) cc_final: 0.7379 (p0) REVERT: A 142 LEU cc_start: 0.8013 (tp) cc_final: 0.7768 (tp) REVERT: A 149 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5688 (m-80) REVERT: B 149 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: B 203 MET cc_start: 0.7849 (mmm) cc_final: 0.7453 (tpp) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 0.1756 time to fit residues: 21.7358 Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5064 Z= 0.264 Angle : 0.705 11.886 6844 Z= 0.372 Chirality : 0.041 0.168 748 Planarity : 0.004 0.026 844 Dihedral : 6.288 53.116 648 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.04 % Allowed : 18.66 % Favored : 76.31 % 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: 2.15 (0.34), residues: 578 helix: 1.77 (0.22), residues: 496 sheet: None (None), residues: 0 loop : -0.56 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 12 HIS 0.007 0.002 HIS A 13 PHE 0.011 0.001 PHE B 222 TYR 0.015 0.002 TYR A 235 ARG 0.005 0.001 ARG A 63 *********************** 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 106 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8302 (t0) cc_final: 0.7188 (p0) REVERT: A 142 LEU cc_start: 0.8090 (tp) cc_final: 0.7864 (tp) REVERT: A 149 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5518 (m-80) REVERT: B 111 ASN cc_start: 0.8127 (t0) cc_final: 0.7039 (p0) REVERT: B 149 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5944 (m-80) REVERT: B 203 MET cc_start: 0.7915 (mmm) cc_final: 0.7376 (tpp) REVERT: B 290 PHE cc_start: 0.6247 (t80) cc_final: 0.5919 (t80) outliers start: 27 outliers final: 17 residues processed: 99 average time/residue: 0.1532 time to fit residues: 19.9845 Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 78 GLN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5064 Z= 0.173 Angle : 0.658 11.908 6844 Z= 0.336 Chirality : 0.038 0.186 748 Planarity : 0.003 0.023 844 Dihedral : 5.589 55.468 644 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.10 % Allowed : 21.08 % Favored : 74.81 % 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 (0.34), residues: 578 helix: 2.05 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -0.71 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 12 HIS 0.008 0.001 HIS B 279 PHE 0.031 0.001 PHE B 91 TYR 0.009 0.001 TYR B 96 ARG 0.003 0.000 ARG B 86 *********************** 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 102 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8187 (t0) cc_final: 0.7065 (p0) REVERT: A 142 LEU cc_start: 0.7929 (tp) cc_final: 0.7703 (tp) REVERT: A 149 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: B 111 ASN cc_start: 0.8159 (t0) cc_final: 0.6980 (p0) REVERT: B 149 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5671 (m-80) outliers start: 22 outliers final: 13 residues processed: 93 average time/residue: 0.1583 time to fit residues: 19.3217 Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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** ** 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: 0.7263 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5064 Z= 0.322 Angle : 0.781 10.471 6844 Z= 0.410 Chirality : 0.044 0.199 748 Planarity : 0.004 0.030 844 Dihedral : 5.501 53.658 643 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.04 % Allowed : 21.83 % Favored : 73.13 % 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: 2.02 (0.34), residues: 578 helix: 1.73 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -0.89 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 12 HIS 0.009 0.002 HIS B 13 PHE 0.023 0.002 PHE A 90 TYR 0.026 0.002 TYR A 234 ARG 0.006 0.001 ARG A 86 *********************** 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 105 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8261 (t0) cc_final: 0.7120 (p0) REVERT: A 140 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 142 LEU cc_start: 0.8095 (tp) cc_final: 0.7792 (tp) REVERT: A 149 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.5380 (m-80) REVERT: B 96 TYR cc_start: 0.6935 (t80) cc_final: 0.6707 (t80) REVERT: B 111 ASN cc_start: 0.8230 (t0) cc_final: 0.7098 (p0) REVERT: B 140 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7392 (mp) REVERT: B 142 LEU cc_start: 0.8068 (tp) cc_final: 0.7834 (tp) REVERT: B 149 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: B 174 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7482 (ttm170) REVERT: B 203 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: B 234 TYR cc_start: 0.8063 (t80) cc_final: 0.7486 (t80) outliers start: 27 outliers final: 20 residues processed: 98 average time/residue: 0.1520 time to fit residues: 19.7407 Evaluate side-chains 98 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN B 82 ASN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5064 Z= 0.176 Angle : 0.686 11.068 6844 Z= 0.359 Chirality : 0.040 0.216 748 Planarity : 0.003 0.024 844 Dihedral : 5.252 55.915 643 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.66 % Allowed : 24.07 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.34), residues: 578 helix: 1.97 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -0.95 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 12 HIS 0.016 0.002 HIS B 279 PHE 0.018 0.001 PHE A 290 TYR 0.025 0.001 TYR A 29 ARG 0.002 0.000 ARG B 10 *********************** 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 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8173 (t0) cc_final: 0.7004 (p0) REVERT: A 142 LEU cc_start: 0.7933 (tp) cc_final: 0.7646 (tp) REVERT: A 149 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5575 (m-80) REVERT: A 234 TYR cc_start: 0.7802 (t80) cc_final: 0.7303 (t80) REVERT: A 290 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5603 (t80) REVERT: B 111 ASN cc_start: 0.8213 (t0) cc_final: 0.7010 (p0) REVERT: B 149 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: B 203 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: B 290 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5792 (t80) outliers start: 25 outliers final: 15 residues processed: 87 average time/residue: 0.1482 time to fit residues: 17.1865 Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5457 > 50: distance: 99 - 104: 5.884 distance: 104 - 105: 7.791 distance: 105 - 106: 13.767 distance: 105 - 108: 20.536 distance: 106 - 107: 38.603 distance: 106 - 112: 19.505 distance: 108 - 109: 20.325 distance: 109 - 110: 8.528 distance: 109 - 111: 8.657 distance: 112 - 113: 13.698 distance: 113 - 114: 16.807 distance: 113 - 116: 21.495 distance: 114 - 115: 32.691 distance: 114 - 117: 21.270 distance: 115 - 146: 33.129 distance: 117 - 118: 12.938 distance: 118 - 119: 12.491 distance: 118 - 121: 17.869 distance: 119 - 120: 37.473 distance: 119 - 128: 29.238 distance: 120 - 154: 23.902 distance: 121 - 122: 9.884 distance: 122 - 123: 16.572 distance: 122 - 124: 10.073 distance: 123 - 125: 11.473 distance: 124 - 126: 4.539 distance: 125 - 127: 5.701 distance: 126 - 127: 8.597 distance: 128 - 129: 36.747 distance: 129 - 130: 34.187 distance: 129 - 132: 43.623 distance: 130 - 131: 40.060 distance: 130 - 135: 26.583 distance: 131 - 162: 28.149 distance: 132 - 133: 44.779 distance: 132 - 134: 34.976 distance: 135 - 136: 11.621 distance: 136 - 137: 11.704 distance: 136 - 139: 28.807 distance: 137 - 138: 38.510 distance: 137 - 146: 6.614 distance: 138 - 170: 35.642 distance: 139 - 140: 14.648 distance: 140 - 141: 7.481 distance: 140 - 142: 12.642 distance: 141 - 143: 3.776 distance: 142 - 144: 10.175 distance: 143 - 145: 9.235 distance: 144 - 145: 12.138 distance: 146 - 147: 22.551 distance: 147 - 148: 23.589 distance: 147 - 150: 37.296 distance: 148 - 149: 36.854 distance: 148 - 154: 28.694 distance: 149 - 181: 48.232 distance: 150 - 151: 23.782 distance: 151 - 152: 6.707 distance: 151 - 153: 16.965 distance: 154 - 155: 6.456 distance: 155 - 156: 13.360 distance: 155 - 158: 4.780 distance: 156 - 157: 39.248 distance: 156 - 162: 27.885 distance: 157 - 189: 24.542 distance: 158 - 159: 29.512 distance: 158 - 160: 11.979 distance: 159 - 161: 11.160 distance: 162 - 163: 30.788 distance: 163 - 164: 25.616 distance: 163 - 166: 15.270 distance: 164 - 165: 36.228 distance: 164 - 170: 14.179 distance: 166 - 167: 12.144 distance: 167 - 168: 23.880 distance: 167 - 169: 17.743 distance: 170 - 171: 11.344 distance: 171 - 172: 20.441 distance: 171 - 174: 45.568 distance: 172 - 173: 33.440 distance: 172 - 181: 6.780 distance: 173 - 200: 28.545 distance: 174 - 175: 10.689 distance: 175 - 176: 18.427 distance: 175 - 177: 11.525 distance: 176 - 178: 6.767 distance: 177 - 179: 17.059 distance: 178 - 180: 8.731 distance: 179 - 180: 12.165 distance: 181 - 182: 16.746 distance: 182 - 183: 22.239 distance: 182 - 185: 21.015 distance: 183 - 184: 39.264 distance: 183 - 189: 19.984 distance: 185 - 186: 22.764 distance: 186 - 187: 7.901 distance: 186 - 188: 11.446