Starting phenix.real_space_refine on Tue Jun 25 07:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy7_36722/06_2024/8jy7_36722.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.185 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 32 5.16 5 C 4912 2.51 5 N 1116 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "C" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "D" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Time building chain proxies: 4.90, per 1000 atoms: 0.67 Number of scatterers: 7292 At special positions: 0 Unit cell: (92.568, 92.568, 63.84, 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 32 16.00 O 1232 8.00 N 1116 7.00 C 4912 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: 3.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 71 through 98 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 170 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.912A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 226 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 261 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.811A pdb=" N VAL A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 281 " --> pdb=" O GLY A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 288 through 310 Proline residue: A 295 - end of helix Processing helix chain 'B' and resid 72 through 98 Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 135' Processing helix chain 'B' and resid 136 through 139 removed outlier: 3.690A pdb=" N VAL B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 170 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 226 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 261 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.810A pdb=" N VAL B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 281 " --> pdb=" O GLY B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 288 through 310 Proline residue: B 295 - end of helix Processing helix chain 'C' and resid 72 through 98 Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL C 139 " --> pdb=" O GLY C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 170 Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 226 Processing helix chain 'C' and resid 236 through 253 Processing helix chain 'C' and resid 261 through 276 Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.811A pdb=" N VAL C 280 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 281 " --> pdb=" O GLY C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 281' Processing helix chain 'C' and resid 288 through 310 Proline residue: C 295 - end of helix Processing helix chain 'D' and resid 72 through 98 Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 135' Processing helix chain 'D' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 170 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.250A pdb=" N PHE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 226 Processing helix chain 'D' and resid 236 through 253 Processing helix chain 'D' and resid 261 through 276 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.810A pdb=" N VAL D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 281 " --> pdb=" O GLY D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 281' Processing helix chain 'D' and resid 288 through 310 Proline residue: D 295 - end of helix 469 hydrogen bonds defined for protein. 1395 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: 1.91 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2185 1.34 - 1.46: 1524 1.46 - 1.57: 3759 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7520 Sorted by residual: bond pdb=" CA ASN B 137 " pdb=" CB ASN B 137 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.63e-01 bond pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.63e-01 bond pdb=" CA ASN D 137 " pdb=" CB ASN D 137 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.65e-01 bond pdb=" CA ASN C 137 " pdb=" CB ASN C 137 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.31e-01 bond pdb=" CB PRO C 232 " pdb=" CG PRO C 232 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 7.97e-01 ... (remaining 7515 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.27: 264 107.27 - 113.95: 4045 113.95 - 120.63: 3383 120.63 - 127.31: 2496 127.31 - 133.99: 76 Bond angle restraints: 10264 Sorted by residual: angle pdb=" C VAL D 290 " pdb=" CA VAL D 290 " pdb=" CB VAL D 290 " ideal model delta sigma weight residual 114.00 111.46 2.54 1.31e+00 5.83e-01 3.74e+00 angle pdb=" C VAL C 290 " pdb=" CA VAL C 290 " pdb=" CB VAL C 290 " ideal model delta sigma weight residual 114.00 111.48 2.52 1.31e+00 5.83e-01 3.71e+00 angle pdb=" C VAL A 290 " pdb=" CA VAL A 290 " pdb=" CB VAL A 290 " ideal model delta sigma weight residual 114.00 111.50 2.50 1.31e+00 5.83e-01 3.65e+00 angle pdb=" C VAL B 290 " pdb=" CA VAL B 290 " pdb=" CB VAL B 290 " ideal model delta sigma weight residual 114.00 111.53 2.47 1.31e+00 5.83e-01 3.57e+00 angle pdb=" CA TYR A 206 " pdb=" C TYR A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 118.44 121.43 -2.99 1.59e+00 3.96e-01 3.54e+00 ... (remaining 10259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 3569 11.63 - 23.26: 379 23.26 - 34.89: 184 34.89 - 46.51: 24 46.51 - 58.14: 12 Dihedral angle restraints: 4168 sinusoidal: 1472 harmonic: 2696 Sorted by residual: dihedral pdb=" CB MET B 116 " pdb=" CG MET B 116 " pdb=" SD MET B 116 " pdb=" CE MET B 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.14 -58.14 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 116 " pdb=" CG MET A 116 " pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.12 -58.12 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET C 116 " pdb=" CG MET C 116 " pdb=" SD MET C 116 " pdb=" CE MET C 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.12 -58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 626 0.028 - 0.056: 356 0.056 - 0.084: 126 0.084 - 0.112: 32 0.112 - 0.140: 8 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CA TYR A 206 " pdb=" N TYR A 206 " pdb=" C TYR A 206 " pdb=" CB TYR A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA TYR D 206 " pdb=" N TYR D 206 " pdb=" C TYR D 206 " pdb=" CB TYR D 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA TYR C 206 " pdb=" N TYR C 206 " pdb=" C TYR C 206 " pdb=" CB TYR C 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1145 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 148 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 149 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 148 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 149 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 148 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 149 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.018 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2543 2.85 - 3.36: 7318 3.36 - 3.88: 12558 3.88 - 4.39: 13826 4.39 - 4.90: 24561 Nonbonded interactions: 60806 Sorted by model distance: nonbonded pdb=" O SER B 121 " pdb=" OG SER B 125 " model vdw 2.340 2.440 nonbonded pdb=" O SER A 121 " pdb=" OG SER A 125 " model vdw 2.340 2.440 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 125 " model vdw 2.341 2.440 nonbonded pdb=" O SER D 121 " pdb=" OG SER D 125 " model vdw 2.341 2.440 nonbonded pdb=" O ASN B 251 " pdb=" OG1 THR C 94 " model vdw 2.366 2.440 ... (remaining 60801 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' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 3.760 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.420 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.003 0.045 7520 Z= 0.174 Angle : 0.596 5.688 10264 Z= 0.309 Chirality : 0.039 0.140 1148 Planarity : 0.005 0.032 1292 Dihedral : 12.176 58.142 2488 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 960 helix: 1.98 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.001 PHE D 185 TYR 0.019 0.001 TYR B 206 ARG 0.003 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.6788 (t80) cc_final: 0.6427 (t80) REVERT: B 236 TYR cc_start: 0.8098 (p90) cc_final: 0.7878 (p90) REVERT: B 286 TYR cc_start: 0.7484 (m-80) cc_final: 0.7279 (m-10) REVERT: B 304 PHE cc_start: 0.8251 (t80) cc_final: 0.8006 (t80) REVERT: C 205 PHE cc_start: 0.7090 (t80) cc_final: 0.6854 (t80) REVERT: C 236 TYR cc_start: 0.8172 (p90) cc_final: 0.7919 (p90) REVERT: C 308 TYR cc_start: 0.6762 (t80) cc_final: 0.6413 (t80) REVERT: D 100 ASP cc_start: 0.7110 (m-30) cc_final: 0.6887 (m-30) REVERT: D 205 PHE cc_start: 0.7131 (t80) cc_final: 0.6885 (t80) REVERT: D 308 TYR cc_start: 0.6787 (t80) cc_final: 0.6483 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1492 time to fit residues: 42.9671 Evaluate side-chains 158 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7520 Z= 0.227 Angle : 0.574 6.744 10264 Z= 0.289 Chirality : 0.040 0.114 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.058 15.556 1028 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.61 % Allowed : 10.16 % Favored : 87.23 % 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: 0.88 (0.27), residues: 960 helix: 1.42 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 192 HIS 0.004 0.001 HIS C 128 PHE 0.018 0.002 PHE A 304 TYR 0.023 0.002 TYR B 206 ARG 0.003 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 TYR cc_start: 0.8240 (p90) cc_final: 0.7811 (p90) REVERT: C 236 TYR cc_start: 0.8225 (p90) cc_final: 0.7805 (p90) outliers start: 19 outliers final: 15 residues processed: 173 average time/residue: 0.1410 time to fit residues: 35.1941 Evaluate side-chains 168 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 172 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7520 Z= 0.237 Angle : 0.561 6.565 10264 Z= 0.290 Chirality : 0.039 0.114 1148 Planarity : 0.005 0.043 1292 Dihedral : 4.254 14.807 1028 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.92 % Allowed : 14.42 % Favored : 83.65 % 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: 0.64 (0.27), residues: 960 helix: 1.25 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.003 0.001 HIS B 128 PHE 0.023 0.002 PHE B 304 TYR 0.018 0.002 TYR A 151 ARG 0.002 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7399 (m-10) cc_final: 0.6854 (m-80) REVERT: A 308 TYR cc_start: 0.6517 (t80) cc_final: 0.6259 (t80) REVERT: B 236 TYR cc_start: 0.8281 (p90) cc_final: 0.7869 (p90) REVERT: C 236 TYR cc_start: 0.8268 (p90) cc_final: 0.7873 (p90) REVERT: D 106 LEU cc_start: 0.8348 (tt) cc_final: 0.8021 (tp) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.1756 time to fit residues: 40.0864 Evaluate side-chains 167 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7520 Z= 0.191 Angle : 0.521 6.197 10264 Z= 0.268 Chirality : 0.038 0.119 1148 Planarity : 0.005 0.047 1292 Dihedral : 4.179 14.665 1028 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.02 % Allowed : 15.93 % Favored : 81.04 % 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: 0.77 (0.27), residues: 960 helix: 1.39 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 289 HIS 0.004 0.001 HIS A 177 PHE 0.009 0.001 PHE D 160 TYR 0.013 0.001 TYR C 206 ARG 0.002 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7315 (ttpt) cc_final: 0.6874 (mtmm) REVERT: A 286 TYR cc_start: 0.7401 (m-10) cc_final: 0.6860 (m-80) REVERT: B 236 TYR cc_start: 0.8272 (p90) cc_final: 0.7834 (p90) REVERT: C 236 TYR cc_start: 0.8267 (p90) cc_final: 0.7845 (p90) REVERT: D 106 LEU cc_start: 0.8355 (tt) cc_final: 0.8025 (tp) outliers start: 22 outliers final: 12 residues processed: 172 average time/residue: 0.1626 time to fit residues: 38.8401 Evaluate side-chains 170 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 64 optimal weight: 0.0040 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7520 Z= 0.161 Angle : 0.502 5.523 10264 Z= 0.257 Chirality : 0.037 0.112 1148 Planarity : 0.005 0.047 1292 Dihedral : 4.042 14.782 1028 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.57 % Allowed : 15.80 % Favored : 80.63 % 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: 0.98 (0.27), residues: 960 helix: 1.54 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.43 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 289 HIS 0.005 0.001 HIS C 177 PHE 0.024 0.001 PHE A 304 TYR 0.016 0.001 TYR D 206 ARG 0.003 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6809 (mtmm) REVERT: A 237 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: A 286 TYR cc_start: 0.7372 (m-10) cc_final: 0.6834 (m-80) REVERT: B 236 TYR cc_start: 0.8236 (p90) cc_final: 0.7786 (p90) REVERT: C 236 TYR cc_start: 0.8218 (p90) cc_final: 0.7799 (p90) REVERT: C 237 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: D 106 LEU cc_start: 0.8325 (tt) cc_final: 0.7982 (tp) REVERT: D 237 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5898 (mp0) outliers start: 26 outliers final: 16 residues processed: 169 average time/residue: 0.1635 time to fit residues: 39.3894 Evaluate side-chains 178 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 7 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7520 Z= 0.160 Angle : 0.502 5.535 10264 Z= 0.256 Chirality : 0.037 0.111 1148 Planarity : 0.005 0.049 1292 Dihedral : 3.993 15.739 1028 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.88 % Allowed : 16.35 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 960 helix: 1.62 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.28 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 289 HIS 0.005 0.001 HIS B 177 PHE 0.007 0.001 PHE C 160 TYR 0.011 0.001 TYR A 206 ARG 0.003 0.001 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6811 (mtmm) REVERT: A 237 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5903 (mp0) REVERT: A 286 TYR cc_start: 0.7382 (m-10) cc_final: 0.6744 (m-80) REVERT: B 175 LYS cc_start: 0.7403 (mtpt) cc_final: 0.6888 (mtmm) REVERT: B 236 TYR cc_start: 0.8233 (p90) cc_final: 0.7780 (p90) REVERT: C 236 TYR cc_start: 0.8215 (p90) cc_final: 0.7763 (p90) REVERT: C 237 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: D 237 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5888 (mp0) outliers start: 21 outliers final: 13 residues processed: 170 average time/residue: 0.1544 time to fit residues: 36.9864 Evaluate side-chains 178 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.0170 chunk 55 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.181 Angle : 0.520 6.743 10264 Z= 0.265 Chirality : 0.037 0.111 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.069 16.782 1028 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.30 % Allowed : 15.80 % Favored : 80.91 % 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: 1.15 (0.28), residues: 960 helix: 1.60 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 289 HIS 0.006 0.001 HIS D 177 PHE 0.027 0.001 PHE B 304 TYR 0.014 0.001 TYR D 206 ARG 0.003 0.001 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6830 (mtmm) REVERT: A 237 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: A 286 TYR cc_start: 0.7323 (m-10) cc_final: 0.6666 (m-80) REVERT: B 175 LYS cc_start: 0.7374 (mtpt) cc_final: 0.6857 (mtmm) REVERT: B 236 TYR cc_start: 0.8266 (p90) cc_final: 0.7793 (p90) REVERT: C 236 TYR cc_start: 0.8235 (p90) cc_final: 0.7787 (p90) REVERT: C 237 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: D 206 TYR cc_start: 0.7008 (m-80) cc_final: 0.6491 (m-80) REVERT: D 237 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5914 (mp0) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.1506 time to fit residues: 37.6989 Evaluate side-chains 190 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 261 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 chunk 80 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.184 Angle : 0.518 5.519 10264 Z= 0.266 Chirality : 0.037 0.111 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.099 17.473 1028 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.98 % Allowed : 15.93 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 960 helix: 1.62 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 289 HIS 0.005 0.001 HIS A 177 PHE 0.022 0.001 PHE C 205 TYR 0.011 0.001 TYR C 206 ARG 0.002 0.000 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7305 (ttpt) cc_final: 0.6819 (mtmm) REVERT: A 237 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 286 TYR cc_start: 0.7318 (m-10) cc_final: 0.6664 (m-80) REVERT: B 175 LYS cc_start: 0.7381 (mtpt) cc_final: 0.6868 (mtmm) REVERT: B 236 TYR cc_start: 0.8240 (p90) cc_final: 0.7765 (p90) REVERT: B 237 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: C 236 TYR cc_start: 0.8214 (p90) cc_final: 0.7765 (p90) REVERT: C 237 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: C 304 PHE cc_start: 0.8250 (t80) cc_final: 0.8007 (t80) REVERT: D 206 TYR cc_start: 0.7207 (m-80) cc_final: 0.6810 (m-80) REVERT: D 237 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5917 (mp0) REVERT: D 304 PHE cc_start: 0.8210 (t80) cc_final: 0.7950 (t80) outliers start: 29 outliers final: 23 residues processed: 184 average time/residue: 0.1485 time to fit residues: 38.9107 Evaluate side-chains 198 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 261 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.183 Angle : 0.521 6.945 10264 Z= 0.266 Chirality : 0.037 0.112 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.135 18.789 1028 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.16 % Allowed : 16.90 % Favored : 79.95 % 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: 1.19 (0.28), residues: 960 helix: 1.62 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 289 HIS 0.005 0.001 HIS A 177 PHE 0.008 0.001 PHE C 246 TYR 0.014 0.001 TYR D 206 ARG 0.002 0.000 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7296 (ttpt) cc_final: 0.6846 (mtmm) REVERT: A 237 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: A 286 TYR cc_start: 0.7329 (m-10) cc_final: 0.6662 (m-80) REVERT: B 175 LYS cc_start: 0.7346 (mtpt) cc_final: 0.6827 (mtmm) REVERT: B 236 TYR cc_start: 0.8243 (p90) cc_final: 0.7767 (p90) REVERT: B 237 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: C 236 TYR cc_start: 0.8215 (p90) cc_final: 0.7766 (p90) REVERT: C 237 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6000 (mp0) REVERT: C 304 PHE cc_start: 0.8252 (t80) cc_final: 0.8007 (t80) REVERT: D 206 TYR cc_start: 0.6978 (m-80) cc_final: 0.6525 (m-80) REVERT: D 237 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: D 304 PHE cc_start: 0.8211 (t80) cc_final: 0.7945 (t80) outliers start: 23 outliers final: 18 residues processed: 182 average time/residue: 0.1520 time to fit residues: 39.2041 Evaluate side-chains 196 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9055 > 50: distance: 4 - 23: 24.004 distance: 8 - 31: 36.847 distance: 13 - 37: 21.487 distance: 18 - 23: 23.245 distance: 19 - 44: 19.086 distance: 23 - 24: 42.627 distance: 24 - 25: 44.634 distance: 24 - 27: 48.106 distance: 25 - 26: 42.359 distance: 25 - 31: 44.943 distance: 26 - 50: 41.658 distance: 27 - 28: 38.788 distance: 28 - 29: 55.570 distance: 28 - 30: 53.993 distance: 31 - 32: 23.392 distance: 32 - 33: 60.130 distance: 32 - 35: 18.163 distance: 33 - 34: 5.772 distance: 33 - 37: 24.801 distance: 34 - 54: 36.929 distance: 35 - 36: 68.778 distance: 37 - 38: 22.335 distance: 38 - 39: 42.524 distance: 38 - 41: 43.167 distance: 39 - 40: 48.730 distance: 39 - 44: 33.614 distance: 40 - 62: 26.433 distance: 41 - 42: 5.417 distance: 41 - 43: 35.562 distance: 44 - 45: 44.914 distance: 45 - 46: 30.849 distance: 45 - 48: 54.601 distance: 46 - 47: 33.984 distance: 46 - 50: 32.213 distance: 48 - 49: 15.897 distance: 50 - 51: 57.536 distance: 51 - 52: 40.530 distance: 52 - 53: 48.373 distance: 52 - 54: 27.983 distance: 54 - 55: 47.769 distance: 55 - 56: 42.630 distance: 55 - 58: 22.793 distance: 56 - 57: 47.999 distance: 56 - 62: 48.841 distance: 58 - 59: 51.885 distance: 58 - 60: 61.357 distance: 59 - 61: 39.346 distance: 62 - 63: 31.020 distance: 63 - 64: 47.995 distance: 63 - 66: 34.075 distance: 64 - 65: 38.476 distance: 64 - 73: 33.523 distance: 66 - 67: 65.509 distance: 67 - 68: 20.473 distance: 67 - 69: 21.803 distance: 68 - 70: 54.662 distance: 69 - 71: 57.750 distance: 70 - 72: 46.188 distance: 71 - 72: 59.363 distance: 73 - 74: 61.551 distance: 74 - 75: 57.593 distance: 74 - 77: 56.092 distance: 75 - 76: 45.916 distance: 75 - 81: 6.841 distance: 77 - 78: 39.086 distance: 78 - 79: 40.394 distance: 78 - 80: 69.676 distance: 81 - 82: 25.092 distance: 81 - 87: 44.650 distance: 82 - 83: 53.487 distance: 82 - 85: 19.154 distance: 83 - 84: 15.438 distance: 83 - 88: 20.840 distance: 85 - 86: 31.117 distance: 86 - 87: 49.544 distance: 88 - 89: 23.136 distance: 89 - 90: 52.680 distance: 89 - 92: 33.556 distance: 90 - 91: 39.088 distance: 90 - 96: 34.737 distance: 92 - 93: 38.923 distance: 93 - 94: 48.862 distance: 93 - 95: 69.981