Starting phenix.real_space_refine on Wed Aug 5 10:26:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.map" model { file = "/net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qc1_18325/08_2026/8qc1_18325.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 15 5.49 5 S 61 5.16 5 C 6253 2.51 5 N 1404 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9431 Number of models: 1 Model: "" Number of chains: 6 Chain: "M" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3913 Classifications: {'peptide': 503} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 482} Chain: "L" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4856 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 1 Chain: "M" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 388 Unusual residues: {' CA': 1, '3PE': 3, '3PH': 6, 'CDL': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 154 Chain: "L" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 1, '3PH': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9431 At special positions: 0 Unit cell: (82.695, 114.73, 101.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 61 16.00 P 15 15.00 O 1697 8.00 N 1404 7.00 C 6253 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 - 3.00 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: 0.94 Conformation dependent library (CDL) restraints added in 313.8 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 3 sheets defined 82.1% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'M' and resid 3 through 23 Proline residue: M 12 - end of helix Processing helix chain 'M' and resid 27 through 56 removed outlier: 3.575A pdb=" N PHE M 51 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 103 Proline residue: M 97 - end of helix Processing helix chain 'M' and resid 104 through 106 No H-bonds generated for 'chain 'M' and resid 104 through 106' Processing helix chain 'M' and resid 109 through 130 removed outlier: 4.038A pdb=" N PHE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 143 removed outlier: 3.524A pdb=" N GLY M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 155 removed outlier: 3.569A pdb=" N MET M 147 " --> pdb=" O GLY M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 189 removed outlier: 3.941A pdb=" N LEU M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET M 177 " --> pdb=" O GLY M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 Processing helix chain 'M' and resid 215 through 233 Processing helix chain 'M' and resid 241 through 249 removed outlier: 3.828A pdb=" N VAL M 247 " --> pdb=" O PRO M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 260 Processing helix chain 'M' and resid 262 through 272 removed outlier: 3.930A pdb=" N GLY M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 277 Processing helix chain 'M' and resid 277 through 305 Proline residue: M 286 - end of helix Processing helix chain 'M' and resid 308 through 331 removed outlier: 3.771A pdb=" N VAL M 318 " --> pdb=" O ALA M 314 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA M 319 " --> pdb=" O TYR M 315 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR M 323 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL M 324 " --> pdb=" O HIS M 320 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 365 removed outlier: 3.621A pdb=" N PHE M 348 " --> pdb=" O LEU M 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 360 " --> pdb=" O CYS M 356 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG M 363 " --> pdb=" O VAL M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 372 Processing helix chain 'M' and resid 374 through 378 Processing helix chain 'M' and resid 379 through 394 Processing helix chain 'M' and resid 399 through 416 removed outlier: 4.159A pdb=" N VAL M 403 " --> pdb=" O THR M 399 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY M 404 " --> pdb=" O SER M 400 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU M 405 " --> pdb=" O GLY M 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL M 415 " --> pdb=" O GLY M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 425 Processing helix chain 'M' and resid 425 through 443 removed outlier: 3.524A pdb=" N ALA M 431 " --> pdb=" O VAL M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 452 Processing helix chain 'M' and resid 458 through 478 removed outlier: 3.581A pdb=" N PHE M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) Proline residue: M 467 - end of helix Processing helix chain 'M' and resid 479 through 500 removed outlier: 4.321A pdb=" N VAL M 485 " --> pdb=" O LEU M 481 " (cutoff:3.500A) Proline residue: M 488 - end of helix Processing helix chain 'L' and resid 2 through 24 Proline residue: L 9 - end of helix removed outlier: 3.646A pdb=" N TRP L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 50 Processing helix chain 'L' and resid 77 through 102 removed outlier: 4.196A pdb=" N GLY L 100 " --> pdb=" O MET L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 134 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 195 removed outlier: 3.844A pdb=" N GLY L 182 " --> pdb=" O VAL L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 210 removed outlier: 3.707A pdb=" N GLN L 205 " --> pdb=" O GLU L 201 " (cutoff:3.500A) Proline residue: L 207 - end of helix Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.669A pdb=" N GLY L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 251 removed outlier: 4.056A pdb=" N ASP L 250 " --> pdb=" O THR L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 254 No H-bonds generated for 'chain 'L' and resid 252 through 254' Processing helix chain 'L' and resid 255 through 265 removed outlier: 3.501A pdb=" N SER L 259 " --> pdb=" O PRO L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 278 removed outlier: 3.552A pdb=" N ALA L 270 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY L 271 " --> pdb=" O MET L 267 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL L 272 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 Processing helix chain 'L' and resid 285 through 307 Processing helix chain 'L' and resid 312 through 334 Processing helix chain 'L' and resid 336 through 365 removed outlier: 3.697A pdb=" N PHE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 374 Processing helix chain 'L' and resid 381 through 397 Processing helix chain 'L' and resid 407 through 424 removed outlier: 3.621A pdb=" N LEU L 411 " --> pdb=" O PHE L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 451 Processing helix chain 'L' and resid 457 through 464 removed outlier: 3.885A pdb=" N HIS L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 494 Proline residue: L 474 - end of helix removed outlier: 3.567A pdb=" N GLY L 481 " --> pdb=" O VAL L 477 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY L 486 " --> pdb=" O ALA L 482 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET L 487 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY L 491 " --> pdb=" O MET L 487 " (cutoff:3.500A) Proline residue: L 492 - end of helix Processing helix chain 'L' and resid 496 through 504 Processing helix chain 'L' and resid 566 through 573 removed outlier: 3.523A pdb=" N HIS L 572 " --> pdb=" O MET L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 575 through 598 Proline residue: L 582 - end of helix Processing helix chain 'L' and resid 602 through 611 Processing helix chain 'L' and resid 611 through 620 Processing helix chain 'L' and resid 623 through 632 Processing helix chain 'L' and resid 632 through 647 Processing helix chain 'L' and resid 651 through 659 Processing sheet with id=AA1, first strand: chain 'M' and resid 64 through 70 removed outlier: 4.240A pdb=" N VAL M 66 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET M 79 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP M 68 " --> pdb=" O TYR M 77 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR M 77 " --> pdb=" O ASP M 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 55 through 65 removed outlier: 5.584A pdb=" N HIS L 56 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU L 76 " --> pdb=" O HIS L 56 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE L 74 " --> pdb=" O PRO L 58 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA L 70 " --> pdb=" O TRP L 62 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL L 64 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 213 through 216 removed outlier: 3.729A pdb=" N ARG L 219 " --> pdb=" O PHE L 216 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1875 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: 1.28 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.45: 2723 1.45 - 1.57: 5296 1.57 - 1.69: 14 1.69 - 1.82: 125 Bond restraints: 9571 Sorted by residual: bond pdb=" OB5 CDL M 608 " pdb=" PB2 CDL M 608 " ideal model delta sigma weight residual 1.657 1.581 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" OA5 CDL M 608 " pdb=" PA1 CDL M 608 " ideal model delta sigma weight residual 1.651 1.583 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" OA2 CDL M 608 " pdb=" PA1 CDL M 608 " ideal model delta sigma weight residual 1.639 1.579 0.060 2.00e-02 2.50e+03 8.93e+00 bond pdb=" OB2 CDL M 608 " pdb=" PB2 CDL M 608 " ideal model delta sigma weight residual 1.636 1.579 0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" CB3 CDL M 608 " pdb=" OB5 CDL M 608 " ideal model delta sigma weight residual 1.403 1.444 -0.041 2.00e-02 2.50e+03 4.12e+00 ... (remaining 9566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12732 1.90 - 3.80: 134 3.80 - 5.70: 44 5.70 - 7.61: 6 7.61 - 9.51: 4 Bond angle restraints: 12920 Sorted by residual: angle pdb=" N PRO L 454 " pdb=" CD PRO L 454 " pdb=" CG PRO L 454 " ideal model delta sigma weight residual 103.20 97.59 5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" CA PRO L 454 " pdb=" N PRO L 454 " pdb=" CD PRO L 454 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CB MET M 1 " pdb=" CG MET M 1 " pdb=" SD MET M 1 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CB PRO L 454 " pdb=" CG PRO L 454 " pdb=" CD PRO L 454 " ideal model delta sigma weight residual 106.10 97.01 9.09 3.20e+00 9.77e-02 8.07e+00 angle pdb=" CB3 CDL M 608 " pdb=" CB4 CDL M 608 " pdb=" OB6 CDL M 608 " ideal model delta sigma weight residual 109.76 101.34 8.42 3.00e+00 1.11e-01 7.88e+00 ... (remaining 12915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 5258 29.97 - 59.93: 275 59.93 - 89.90: 24 89.90 - 119.87: 6 119.87 - 149.84: 3 Dihedral angle restraints: 5566 sinusoidal: 2353 harmonic: 3213 Sorted by residual: dihedral pdb=" CA ALA L 265 " pdb=" C ALA L 265 " pdb=" N THR L 266 " pdb=" CA THR L 266 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CB P5S L 802 " pdb=" OG P5S L 802 " pdb=" P12 P5S L 802 " pdb=" O16 P5S L 802 " ideal model delta sinusoidal sigma weight residual 295.68 145.84 149.84 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C27 P5S L 802 " pdb=" C28 P5S L 802 " pdb=" C29 P5S L 802 " pdb=" C30 P5S L 802 " ideal model delta sinusoidal sigma weight residual 298.90 171.08 127.82 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 5563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1253 0.063 - 0.127: 145 0.127 - 0.190: 3 0.190 - 0.253: 1 0.253 - 0.317: 2 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB4 CDL M 608 " pdb=" CB3 CDL M 608 " pdb=" CB6 CDL M 608 " pdb=" OB6 CDL M 608 " both_signs ideal model delta sigma weight residual False -2.61 -2.92 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA4 CDL M 608 " pdb=" CA3 CDL M 608 " pdb=" CA6 CDL M 608 " pdb=" OA6 CDL M 608 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2 P5S L 802 " pdb=" C1 P5S L 802 " pdb=" C3 P5S L 802 " pdb=" O37 P5S L 802 " both_signs ideal model delta sigma weight residual False 2.59 2.34 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1401 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 113 " 0.019 2.00e-02 2.50e+03 1.40e-02 3.92e+00 pdb=" CG TYR M 113 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR M 113 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR M 113 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR M 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR M 113 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 113 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 113 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 160 " -0.010 2.00e-02 2.50e+03 1.25e-02 3.13e+00 pdb=" CG TYR L 160 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR L 160 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR L 160 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR L 160 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 160 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 160 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY L 491 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO L 492 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO L 492 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 492 " -0.017 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 55 2.46 - 3.07: 6468 3.07 - 3.68: 14733 3.68 - 4.29: 24354 4.29 - 4.90: 38798 Nonbonded interactions: 84408 Sorted by model distance: nonbonded pdb=" O GLU L 368 " pdb=" OH TYR L 374 " model vdw 1.851 3.040 nonbonded pdb=" O ALA M 331 " pdb=" O HOH M 701 " model vdw 1.983 3.040 nonbonded pdb=" O HOH M 727 " pdb=" O HOH M 737 " model vdw 1.991 3.040 nonbonded pdb=" O HIS L 69 " pdb=" O HOH L 901 " model vdw 2.003 3.040 nonbonded pdb=" O ALA L 435 " pdb=" O HOH L 902 " model vdw 2.045 3.040 ... (remaining 84403 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: 17.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 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 0.076 9571 Z= 0.195 Angle : 0.591 9.506 12920 Z= 0.281 Chirality : 0.041 0.317 1404 Planarity : 0.003 0.030 1541 Dihedral : 17.817 149.835 3512 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.45 % Allowed : 4.01 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1112 helix: 0.98 (0.18), residues: 805 sheet: 1.17 (1.18), residues: 20 loop : -0.74 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 378 TYR 0.034 0.002 TYR M 113 PHE 0.016 0.001 PHE L 350 TRP 0.010 0.001 TRP M 241 HIS 0.004 0.001 HIS L 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 9571) covalent geometry : angle 0.59062 / 0.28 (12920) hydrogen bonds : bond 0.22686 / 15.32 ( 634) hydrogen bonds : angle 7.73380 / 5.53 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.247 Fit side-chains REVERT: M 1 MET cc_start: 0.5267 (tmm) cc_final: 0.4727 (mpp) outliers start: 4 outliers final: 0 residues processed: 91 average time/residue: 0.6358 time to fit residues: 61.3644 Evaluate side-chains 84 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0050 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 366 HIS L 373 ASN L 458 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.078627 restraints weight = 12710.890| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.25 r_work: 0.2821 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9571 Z= 0.143 Angle : 0.567 6.919 12920 Z= 0.299 Chirality : 0.043 0.174 1404 Planarity : 0.004 0.032 1541 Dihedral : 15.949 150.091 1644 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.78 % Allowed : 4.57 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1112 helix: 1.72 (0.17), residues: 820 sheet: 1.43 (1.26), residues: 20 loop : -0.76 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 55 TYR 0.030 0.002 TYR M 113 PHE 0.031 0.001 PHE L 350 TRP 0.015 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 9571) covalent geometry : angle 0.56699 / 0.30 (12920) hydrogen bonds : bond 0.05441 / 3.71 ( 634) hydrogen bonds : angle 5.01174 / 3.65 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.290 Fit side-chains REVERT: M 79 MET cc_start: 0.9160 (mtt) cc_final: 0.8739 (mtp) REVERT: M 141 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5222 (mm-30) REVERT: L 414 ASP cc_start: 0.8393 (m-30) cc_final: 0.7888 (t0) outliers start: 16 outliers final: 1 residues processed: 106 average time/residue: 0.5927 time to fit residues: 67.2971 Evaluate side-chains 87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 373 ASN L 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079368 restraints weight = 12617.583| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.25 r_work: 0.2831 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9571 Z= 0.124 Angle : 0.507 7.159 12920 Z= 0.268 Chirality : 0.040 0.162 1404 Planarity : 0.004 0.029 1541 Dihedral : 14.949 155.835 1644 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.67 % Allowed : 5.35 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1112 helix: 1.94 (0.18), residues: 824 sheet: 1.74 (1.30), residues: 20 loop : -0.67 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 55 TYR 0.025 0.002 TYR M 113 PHE 0.029 0.001 PHE L 350 TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9571) covalent geometry : angle 0.50660 / 0.27 (12920) hydrogen bonds : bond 0.05187 / 3.53 ( 634) hydrogen bonds : angle 4.73149 / 3.45 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.249 Fit side-chains REVERT: M 79 MET cc_start: 0.9143 (mtt) cc_final: 0.8733 (mtp) REVERT: M 141 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5129 (mm-30) REVERT: M 157 LYS cc_start: 0.8718 (mppt) cc_final: 0.8228 (mptt) REVERT: L 368 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: L 414 ASP cc_start: 0.8427 (m-30) cc_final: 0.7905 (t0) outliers start: 15 outliers final: 3 residues processed: 98 average time/residue: 0.6202 time to fit residues: 64.6697 Evaluate side-chains 87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 402 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.076604 restraints weight = 12796.197| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.25 r_work: 0.2787 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9571 Z= 0.152 Angle : 0.545 7.337 12920 Z= 0.287 Chirality : 0.042 0.181 1404 Planarity : 0.004 0.030 1541 Dihedral : 15.070 151.003 1644 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.23 % Allowed : 5.79 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1112 helix: 1.82 (0.18), residues: 823 sheet: 1.66 (1.26), residues: 20 loop : -0.81 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 21 TYR 0.025 0.002 TYR M 113 PHE 0.026 0.001 PHE L 350 TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9571) covalent geometry : angle 0.54504 / 0.29 (12920) hydrogen bonds : bond 0.05604 / 3.81 ( 634) hydrogen bonds : angle 4.81100 / 3.51 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.405 Fit side-chains REVERT: M 1 MET cc_start: 0.5068 (tmm) cc_final: 0.4454 (mpp) REVERT: M 79 MET cc_start: 0.9144 (mtt) cc_final: 0.8707 (mtp) REVERT: M 105 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: M 141 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5123 (mm-30) REVERT: M 157 LYS cc_start: 0.8771 (mppt) cc_final: 0.8299 (mptt) REVERT: L 26 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8536 (ttpp) REVERT: L 368 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: L 414 ASP cc_start: 0.8485 (m-30) cc_final: 0.7950 (t0) outliers start: 20 outliers final: 4 residues processed: 97 average time/residue: 0.5914 time to fit residues: 61.1483 Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 424 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 6 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080611 restraints weight = 12883.266| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.27 r_work: 0.2860 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9571 Z= 0.110 Angle : 0.481 5.576 12920 Z= 0.254 Chirality : 0.040 0.167 1404 Planarity : 0.004 0.033 1541 Dihedral : 14.495 154.094 1644 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.45 % Allowed : 7.02 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.25), residues: 1112 helix: 2.10 (0.18), residues: 813 sheet: 1.75 (1.30), residues: 20 loop : -0.51 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 75 TYR 0.023 0.001 TYR M 433 PHE 0.029 0.001 PHE L 350 TRP 0.015 0.001 TRP L 145 HIS 0.004 0.001 HIS L 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 9571) covalent geometry : angle 0.48147 / 0.25 (12920) hydrogen bonds : bond 0.04449 / 3.05 ( 634) hydrogen bonds : angle 4.58230 / 3.35 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.353 Fit side-chains REVERT: M 1 MET cc_start: 0.4972 (tmm) cc_final: 0.4464 (mpp) REVERT: M 79 MET cc_start: 0.9093 (mtt) cc_final: 0.8680 (mtp) REVERT: M 105 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: M 141 GLU cc_start: 0.6295 (pp20) cc_final: 0.4968 (mm-30) REVERT: M 157 LYS cc_start: 0.8722 (mppt) cc_final: 0.8243 (mptt) REVERT: L 21 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7818 (mtm-85) REVERT: L 26 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8510 (ttpp) REVERT: L 208 GLN cc_start: 0.7815 (mm110) cc_final: 0.7145 (mm-40) REVERT: L 365 MET cc_start: 0.8863 (mmm) cc_final: 0.8544 (mmm) REVERT: L 368 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: L 414 ASP cc_start: 0.8443 (m-30) cc_final: 0.7904 (t0) outliers start: 13 outliers final: 3 residues processed: 96 average time/residue: 0.6807 time to fit residues: 69.4161 Evaluate side-chains 88 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.8416 > 50:) chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077668 restraints weight = 12863.029| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.26 r_work: 0.2802 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9571 Z= 0.138 Angle : 0.522 5.610 12920 Z= 0.275 Chirality : 0.041 0.177 1404 Planarity : 0.004 0.032 1541 Dihedral : 14.480 151.727 1644 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.56 % Allowed : 7.80 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1112 helix: 1.94 (0.18), residues: 823 sheet: 1.75 (1.28), residues: 20 loop : -0.80 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 480 TYR 0.023 0.002 TYR L 426 PHE 0.026 0.001 PHE L 350 TRP 0.012 0.001 TRP L 145 HIS 0.004 0.001 HIS L 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 9571) covalent geometry : angle 0.52207 / 0.27 (12920) hydrogen bonds : bond 0.05233 / 3.57 ( 634) hydrogen bonds : angle 4.69316 / 3.43 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.268 Fit side-chains REVERT: M 1 MET cc_start: 0.5099 (tmm) cc_final: 0.4615 (mpp) REVERT: M 79 MET cc_start: 0.9118 (mtt) cc_final: 0.8858 (mtt) REVERT: M 105 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: M 141 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.4896 (mm-30) REVERT: M 157 LYS cc_start: 0.8734 (mppt) cc_final: 0.8265 (mptt) REVERT: L 208 GLN cc_start: 0.7838 (mm110) cc_final: 0.7155 (mm-40) REVERT: L 368 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (tm-30) outliers start: 14 outliers final: 4 residues processed: 93 average time/residue: 0.6872 time to fit residues: 67.9081 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.079844 restraints weight = 12805.811| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.27 r_work: 0.2843 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9571 Z= 0.115 Angle : 0.490 5.501 12920 Z= 0.258 Chirality : 0.040 0.172 1404 Planarity : 0.004 0.032 1541 Dihedral : 14.185 153.588 1644 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.34 % Allowed : 8.57 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.25), residues: 1112 helix: 2.08 (0.18), residues: 814 sheet: 1.84 (1.31), residues: 20 loop : -0.50 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 55 TYR 0.022 0.002 TYR M 433 PHE 0.028 0.001 PHE L 350 TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9571) covalent geometry : angle 0.48973 / 0.26 (12920) hydrogen bonds : bond 0.04655 / 3.19 ( 634) hydrogen bonds : angle 4.59961 / 3.36 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.215 Fit side-chains REVERT: M 1 MET cc_start: 0.5050 (tmm) cc_final: 0.4591 (mpp) REVERT: M 105 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: M 141 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.4882 (mm-30) REVERT: M 157 LYS cc_start: 0.8724 (mppt) cc_final: 0.8248 (mptt) REVERT: L 26 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: L 208 GLN cc_start: 0.7840 (mm110) cc_final: 0.7168 (mm-40) REVERT: L 368 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: L 414 ASP cc_start: 0.8449 (m-30) cc_final: 0.7832 (t0) outliers start: 12 outliers final: 3 residues processed: 92 average time/residue: 0.6936 time to fit residues: 67.7144 Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.080337 restraints weight = 12740.446| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.27 r_work: 0.2852 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9571 Z= 0.113 Angle : 0.487 5.521 12920 Z= 0.256 Chirality : 0.040 0.171 1404 Planarity : 0.004 0.032 1541 Dihedral : 13.941 152.090 1644 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 8.80 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.25), residues: 1112 helix: 2.12 (0.18), residues: 812 sheet: 1.97 (1.31), residues: 20 loop : -0.49 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 75 TYR 0.023 0.002 TYR L 426 PHE 0.028 0.001 PHE L 350 TRP 0.013 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9571) covalent geometry : angle 0.48702 / 0.26 (12920) hydrogen bonds : bond 0.04579 / 3.13 ( 634) hydrogen bonds : angle 4.56753 / 3.34 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.361 Fit side-chains REVERT: M 1 MET cc_start: 0.5038 (tmm) cc_final: 0.4605 (mpp) REVERT: M 105 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: M 141 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.4836 (mm-30) REVERT: M 157 LYS cc_start: 0.8714 (mppt) cc_final: 0.8238 (mptt) REVERT: L 26 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: L 208 GLN cc_start: 0.7826 (mm110) cc_final: 0.7154 (mm-40) outliers start: 11 outliers final: 2 residues processed: 89 average time/residue: 0.6432 time to fit residues: 60.7285 Evaluate side-chains 87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.075687 restraints weight = 12824.401| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.26 r_work: 0.2767 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9571 Z= 0.175 Angle : 0.568 5.724 12920 Z= 0.300 Chirality : 0.043 0.187 1404 Planarity : 0.004 0.032 1541 Dihedral : 14.530 148.930 1644 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.22 % Allowed : 8.91 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1112 helix: 1.74 (0.18), residues: 828 sheet: 1.89 (1.31), residues: 20 loop : -0.81 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 76 TYR 0.024 0.002 TYR L 426 PHE 0.025 0.002 PHE L 350 TRP 0.010 0.001 TRP M 290 HIS 0.004 0.001 HIS L 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 9571) covalent geometry : angle 0.56802 / 0.30 (12920) hydrogen bonds : bond 0.05947 / 4.04 ( 634) hydrogen bonds : angle 4.84421 / 3.54 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.330 Fit side-chains REVERT: M 1 MET cc_start: 0.5337 (tmm) cc_final: 0.4829 (mpp) REVERT: M 105 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: M 141 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.4829 (mm-30) REVERT: M 157 LYS cc_start: 0.8765 (mppt) cc_final: 0.8310 (mptt) REVERT: L 26 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: L 208 GLN cc_start: 0.7852 (mm110) cc_final: 0.7156 (mm-40) REVERT: L 414 ASP cc_start: 0.8527 (m-30) cc_final: 0.7946 (t0) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 0.6307 time to fit residues: 61.1841 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.078462 restraints weight = 12836.915| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.26 r_work: 0.2818 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9571 Z= 0.126 Angle : 0.508 5.532 12920 Z= 0.269 Chirality : 0.041 0.176 1404 Planarity : 0.004 0.031 1541 Dihedral : 14.132 151.452 1644 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.00 % Allowed : 9.24 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1112 helix: 1.94 (0.18), residues: 819 sheet: 1.79 (1.30), residues: 20 loop : -0.61 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 455 TYR 0.022 0.002 TYR L 426 PHE 0.027 0.001 PHE L 350 TRP 0.012 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9571) covalent geometry : angle 0.50772 / 0.27 (12920) hydrogen bonds : bond 0.04945 / 3.38 ( 634) hydrogen bonds : angle 4.67749 / 3.42 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.300 Fit side-chains REVERT: M 1 MET cc_start: 0.5325 (tmm) cc_final: 0.4811 (mpp) REVERT: M 105 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: M 141 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.4827 (mm-30) REVERT: M 157 LYS cc_start: 0.8751 (mppt) cc_final: 0.8299 (mptt) REVERT: L 26 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: L 208 GLN cc_start: 0.7833 (mm110) cc_final: 0.7155 (mm-40) REVERT: L 414 ASP cc_start: 0.8494 (m-30) cc_final: 0.7903 (t0) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 0.7005 time to fit residues: 67.0763 Evaluate side-chains 88 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.092433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.079800 restraints weight = 12743.521| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.26 r_work: 0.2842 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9571 Z= 0.116 Angle : 0.494 5.517 12920 Z= 0.260 Chirality : 0.040 0.170 1404 Planarity : 0.004 0.031 1541 Dihedral : 13.779 151.086 1644 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.00 % Allowed : 9.35 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.25), residues: 1112 helix: 2.08 (0.18), residues: 814 sheet: 1.86 (1.30), residues: 20 loop : -0.48 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 55 TYR 0.022 0.002 TYR L 426 PHE 0.028 0.001 PHE L 350 TRP 0.013 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9571) covalent geometry : angle 0.49405 / 0.26 (12920) hydrogen bonds : bond 0.04635 / 3.17 ( 634) hydrogen bonds : angle 4.59408 / 3.36 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.72 seconds wall clock time: 54 minutes 7.98 seconds (3247.98 seconds total)