Starting phenix.real_space_refine on Thu Nov 14 12:48:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrd_37774/11_2024/8wrd_37774.cif" } resolution = 3.05 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= 1.000 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 42 5.16 5 C 4078 2.51 5 N 1017 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6326 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2957 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 23, 'TRANS': 369} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Time building chain proxies: 4.48, per 1000 atoms: 0.71 Number of scatterers: 6326 At special positions: 0 Unit cell: (84.48, 84.48, 132, 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 42 16.00 O 1189 8.00 N 1017 7.00 C 4078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 46.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.733A pdb=" N TRP A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.807A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.815A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.707A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.731A pdb=" N ARG A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.549A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.714A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.295A pdb=" N ALA A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.860A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.777A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.610A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.518A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.924A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.939A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.975A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.522A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.548A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.847A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.767A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.514A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.676A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.583A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.589A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.508A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.589A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 118 removed outlier: 3.862A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.593A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.693A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA H 110 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.627A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1041 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: 2.04 Time building geometry restraints manager: 1.96 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: 1957 1.34 - 1.46: 1540 1.46 - 1.58: 2914 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6478 Sorted by residual: bond pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.37e-02 5.33e+03 8.60e-01 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.31e-01 bond pdb=" CB ASP H 103 " pdb=" CG ASP H 103 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.12e-01 bond pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 bond pdb=" CB VAL L 146 " pdb=" CG2 VAL L 146 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8657 1.61 - 3.23: 121 3.23 - 4.84: 28 4.84 - 6.45: 9 6.45 - 8.06: 1 Bond angle restraints: 8816 Sorted by residual: angle pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.41e+00 angle pdb=" N GLY A 436 " pdb=" CA GLY A 436 " pdb=" C GLY A 436 " ideal model delta sigma weight residual 112.34 117.07 -4.73 2.04e+00 2.40e-01 5.39e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.28 -2.58 1.22e+00 6.72e-01 4.48e+00 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.42 113.57 -3.15 1.49e+00 4.50e-01 4.47e+00 ... (remaining 8811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3344 17.15 - 34.30: 374 34.30 - 51.45: 98 51.45 - 68.61: 18 68.61 - 85.76: 6 Dihedral angle restraints: 3840 sinusoidal: 1451 harmonic: 2389 Sorted by residual: dihedral pdb=" CA LYS H 126 " pdb=" C LYS H 126 " pdb=" N THR H 127 " pdb=" CA THR H 127 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU L 136 " pdb=" C LEU L 136 " pdb=" N ASN L 137 " pdb=" CA ASN L 137 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 58.97 34.03 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 604 0.029 - 0.058: 260 0.058 - 0.087: 87 0.087 - 0.116: 59 0.116 - 0.145: 8 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE L 144 " pdb=" N ILE L 144 " pdb=" C ILE L 144 " pdb=" CB ILE L 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1015 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 126 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS H 126 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 126 " -0.014 2.00e-02 2.50e+03 pdb=" N THR H 127 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 386 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 387 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.023 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 265 2.72 - 3.27: 6059 3.27 - 3.81: 10078 3.81 - 4.36: 12165 4.36 - 4.90: 22210 Nonbonded interactions: 50777 Sorted by model distance: nonbonded pdb=" O ASN L 137 " pdb=" OG SER L 174 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 291 " pdb=" NE2 HIS A 414 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.310 3.120 nonbonded pdb=" O GLU L 123 " pdb=" OG1 THR L 126 " model vdw 2.316 3.040 ... (remaining 50772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.930 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.033 6478 Z= 0.234 Angle : 0.552 8.063 8816 Z= 0.285 Chirality : 0.042 0.145 1018 Planarity : 0.004 0.044 1103 Dihedral : 15.710 85.756 2300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 22.33 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.84 (0.30), residues: 822 helix: 1.34 (0.30), residues: 329 sheet: 1.38 (0.36), residues: 221 loop : -1.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE L 87 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG L 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.796 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2406 time to fit residues: 19.8063 Evaluate side-chains 61 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN L 77 ASN L 210 ASN H 5 GLN H 59 ASN H 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6478 Z= 0.205 Angle : 0.548 6.096 8816 Z= 0.286 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.420 22.415 884 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.28 % Allowed : 21.34 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.90 (0.30), residues: 822 helix: 1.34 (0.30), residues: 334 sheet: 1.28 (0.36), residues: 217 loop : -0.90 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.688 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.2223 time to fit residues: 21.5858 Evaluate side-chains 65 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6478 Z= 0.208 Angle : 0.536 6.153 8816 Z= 0.277 Chirality : 0.041 0.135 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.402 23.770 884 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.84 % Allowed : 21.05 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.30), residues: 822 helix: 1.38 (0.30), residues: 333 sheet: 1.21 (0.35), residues: 222 loop : -0.98 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.700 Fit side-chains REVERT: L 6 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: H 89 ASP cc_start: 0.8352 (t0) cc_final: 0.8103 (t0) outliers start: 20 outliers final: 11 residues processed: 85 average time/residue: 0.1888 time to fit residues: 21.6928 Evaluate side-chains 75 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6478 Z= 0.188 Angle : 0.524 6.352 8816 Z= 0.270 Chirality : 0.041 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.318 23.311 884 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.41 % Allowed : 20.91 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.93 (0.30), residues: 822 helix: 1.48 (0.30), residues: 332 sheet: 1.22 (0.35), residues: 222 loop : -1.00 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.008 0.001 TYR L 49 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.811 Fit side-chains REVERT: L 6 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: H 89 ASP cc_start: 0.8326 (t0) cc_final: 0.8089 (t0) outliers start: 24 outliers final: 17 residues processed: 90 average time/residue: 0.2087 time to fit residues: 25.2576 Evaluate side-chains 84 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6478 Z= 0.236 Angle : 0.543 6.312 8816 Z= 0.279 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.392 22.946 884 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.41 % Allowed : 20.20 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.85 (0.30), residues: 822 helix: 1.38 (0.30), residues: 332 sheet: 1.17 (0.35), residues: 222 loop : -0.98 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.002 0.001 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.010 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.806 Fit side-chains REVERT: L 6 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: H 89 ASP cc_start: 0.8349 (t0) cc_final: 0.8143 (t0) outliers start: 31 outliers final: 24 residues processed: 92 average time/residue: 0.1748 time to fit residues: 21.8932 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6478 Z= 0.229 Angle : 0.543 6.968 8816 Z= 0.280 Chirality : 0.042 0.138 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.406 24.107 884 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.13 % Allowed : 20.48 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.84 (0.30), residues: 822 helix: 1.39 (0.30), residues: 331 sheet: 1.15 (0.35), residues: 222 loop : -1.00 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.002 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.010 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.690 Fit side-chains REVERT: A 244 GLU cc_start: 0.7585 (pp20) cc_final: 0.7043 (tm-30) REVERT: L 6 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8400 (tt0) outliers start: 29 outliers final: 24 residues processed: 91 average time/residue: 0.1829 time to fit residues: 22.8239 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6478 Z= 0.275 Angle : 0.569 7.196 8816 Z= 0.294 Chirality : 0.043 0.134 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.520 24.024 884 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.84 % Allowed : 19.91 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.76 (0.30), residues: 822 helix: 1.30 (0.30), residues: 331 sheet: 1.11 (0.35), residues: 224 loop : -1.02 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 114 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE L 87 TYR 0.011 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.740 Fit side-chains REVERT: A 244 GLU cc_start: 0.7567 (pp20) cc_final: 0.7133 (tm-30) REVERT: L 6 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8430 (tt0) outliers start: 34 outliers final: 27 residues processed: 95 average time/residue: 0.1732 time to fit residues: 22.4451 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6478 Z= 0.215 Angle : 0.545 7.494 8816 Z= 0.282 Chirality : 0.042 0.139 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.439 23.982 884 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.41 % Allowed : 20.48 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.79 (0.30), residues: 822 helix: 1.38 (0.30), residues: 331 sheet: 1.05 (0.34), residues: 224 loop : -1.01 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.755 Fit side-chains REVERT: A 244 GLU cc_start: 0.7570 (pp20) cc_final: 0.7150 (tm-30) REVERT: L 6 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8423 (tt0) outliers start: 31 outliers final: 28 residues processed: 92 average time/residue: 0.1768 time to fit residues: 22.1060 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0002 > 50: distance: 66 - 70: 27.794 distance: 70 - 71: 28.647 distance: 71 - 72: 25.936 distance: 71 - 74: 9.877 distance: 72 - 73: 20.406 distance: 72 - 78: 36.711 distance: 74 - 75: 26.711 distance: 75 - 76: 18.436 distance: 75 - 77: 31.351 distance: 78 - 79: 9.714 distance: 79 - 80: 9.164 distance: 79 - 82: 14.748 distance: 80 - 81: 20.341 distance: 80 - 84: 18.696 distance: 82 - 83: 10.716 distance: 84 - 85: 13.459 distance: 85 - 86: 9.946 distance: 85 - 88: 15.209 distance: 86 - 87: 25.833 distance: 86 - 90: 37.387 distance: 88 - 89: 14.105 distance: 90 - 91: 10.065 distance: 91 - 92: 7.779 distance: 92 - 93: 34.768 distance: 92 - 94: 14.836 distance: 94 - 95: 5.819 distance: 95 - 96: 6.217 distance: 95 - 98: 8.219 distance: 96 - 97: 10.363 distance: 96 - 101: 3.359 distance: 98 - 99: 10.266 distance: 98 - 100: 7.536 distance: 101 - 102: 5.574 distance: 101 - 177: 9.956 distance: 102 - 103: 13.456 distance: 102 - 105: 5.975 distance: 103 - 104: 10.328 distance: 103 - 111: 17.667 distance: 104 - 174: 14.411 distance: 106 - 107: 3.516 distance: 107 - 109: 4.501 distance: 108 - 110: 3.430 distance: 111 - 112: 16.283 distance: 112 - 113: 34.594 distance: 112 - 115: 17.496 distance: 113 - 114: 21.496 distance: 113 - 118: 24.166 distance: 115 - 116: 21.828 distance: 115 - 117: 14.007 distance: 118 - 119: 8.252 distance: 119 - 120: 19.186 distance: 119 - 122: 32.577 distance: 120 - 121: 34.289 distance: 120 - 129: 10.178 distance: 122 - 123: 25.933 distance: 123 - 124: 30.419 distance: 123 - 125: 10.476 distance: 124 - 126: 21.971 distance: 125 - 127: 19.454 distance: 126 - 128: 18.920 distance: 127 - 128: 23.461 distance: 129 - 130: 9.382 distance: 129 - 135: 9.509 distance: 130 - 131: 33.615 distance: 130 - 133: 17.912 distance: 131 - 132: 5.380 distance: 131 - 136: 31.540 distance: 133 - 134: 12.905 distance: 134 - 135: 26.492 distance: 136 - 137: 13.241 distance: 137 - 138: 21.161 distance: 137 - 140: 6.375 distance: 138 - 139: 7.251 distance: 138 - 141: 13.263