Starting phenix.real_space_refine on Fri Mar 14 01:51:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qc1_18325/03_2025/8qc1_18325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qc1_18325/03_2025/8qc1_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_18325/03_2025/8qc1_18325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qc1_18325/03_2025/8qc1_18325.map" model { file = "/net/cci-nas-00/data/ceres_data/8qc1_18325/03_2025/8qc1_18325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qc1_18325/03_2025/8qc1_18325.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 11.45, per 1000 atoms: 1.21 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.87 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: 2.94 Time building geometry restraints manager: 3.09 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=" N MET L 1 " pdb=" CA MET L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N MET M 1 " pdb=" CA MET M 1 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.04e+00 bond pdb=" C20 P5S L 802 " pdb=" C21 P5S L 802 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C17 P5S L 802 " pdb=" O19 P5S L 802 " ideal model delta sigma weight residual 1.351 1.326 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CB P5S L 802 " pdb=" OG P5S L 802 " ideal model delta sigma weight residual 1.436 1.411 0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 9566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12754 1.90 - 3.80: 119 3.80 - 5.70: 39 5.70 - 7.61: 5 7.61 - 9.51: 3 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 107.81 101.34 6.47 2.43e+00 1.69e-01 7.10e+00 ... (remaining 12915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 5312 31.05 - 62.11: 273 62.11 - 93.16: 29 93.16 - 124.21: 5 124.21 - 155.27: 3 Dihedral angle restraints: 5622 sinusoidal: 2409 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=" CA5 CDL M 608 " pdb=" CA4 CDL M 608 " pdb=" OA6 CDL M 608 " pdb=" CA6 CDL M 608 " ideal model delta sinusoidal sigma weight residual 168.24 -36.49 -155.27 1 3.00e+01 1.11e-03 2.04e+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 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1300 0.070 - 0.139: 101 0.139 - 0.209: 0 0.209 - 0.278: 2 0.278 - 0.348: 1 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 -2.57 -2.92 0.35 2.00e-01 2.50e+01 3.02e+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 -2.57 -2.84 0.27 2.00e-01 2.50e+01 1.77e+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: 375.770 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 421.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 0.036 9571 Z= 0.255 Angle : 0.567 9.506 12920 Z= 0.278 Chirality : 0.041 0.348 1404 Planarity : 0.003 0.030 1541 Dihedral : 18.500 155.267 3568 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.92 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 (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 (0.25), 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 TRP 0.010 0.001 TRP M 241 HIS 0.004 0.001 HIS L 404 PHE 0.016 0.001 PHE L 350 TYR 0.034 0.002 TYR M 113 ARG 0.004 0.001 ARG L 378 *********************** 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 : 0.914 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: 1.5636 time to fit residues: 151.2096 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3114 r_free = 0.3114 target = 0.090452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077703 restraints weight = 12583.641| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.24 r_work: 0.2805 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9571 Z= 0.202 Angle : 0.569 6.764 12920 Z= 0.301 Chirality : 0.042 0.170 1404 Planarity : 0.004 0.031 1541 Dihedral : 17.586 153.983 1700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.89 % Allowed : 4.57 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1112 helix: 1.73 (0.17), residues: 819 sheet: 1.41 (1.25), residues: 20 loop : -0.78 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.031 0.001 PHE L 350 TYR 0.029 0.002 TYR M 113 ARG 0.004 0.000 ARG L 55 *********************** 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 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.886 Fit side-chains REVERT: M 79 MET cc_start: 0.9163 (mtt) cc_final: 0.8758 (mtp) REVERT: M 141 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5402 (pp20) REVERT: L 26 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8617 (ttpp) REVERT: L 414 ASP cc_start: 0.8408 (m-30) cc_final: 0.7914 (t0) outliers start: 17 outliers final: 2 residues processed: 104 average time/residue: 1.4309 time to fit residues: 158.5642 Evaluate side-chains 88 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.078692 restraints weight = 12727.952| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.26 r_work: 0.2819 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9571 Z= 0.169 Angle : 0.515 7.320 12920 Z= 0.272 Chirality : 0.041 0.167 1404 Planarity : 0.004 0.030 1541 Dihedral : 16.578 155.417 1700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.89 % Allowed : 5.01 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1112 helix: 1.91 (0.18), residues: 824 sheet: 1.72 (1.29), residues: 20 loop : -0.72 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.029 0.001 PHE L 350 TYR 0.024 0.002 TYR M 113 ARG 0.002 0.000 ARG L 55 *********************** 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 107 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 2.533 Fit side-chains REVERT: M 79 MET cc_start: 0.9156 (mtt) cc_final: 0.8738 (mtp) REVERT: M 141 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5091 (mm-30) REVERT: M 157 LYS cc_start: 0.8724 (mppt) cc_final: 0.8234 (mptt) REVERT: L 368 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: L 414 ASP cc_start: 0.8428 (m-30) cc_final: 0.7882 (t0) outliers start: 17 outliers final: 3 residues processed: 100 average time/residue: 1.6587 time to fit residues: 175.5925 Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3127 r_free = 0.3127 target = 0.091355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.078560 restraints weight = 12635.123| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.25 r_work: 0.2817 rms_B_bonded: 1.94 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: 0.8830 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9571 Z= 0.172 Angle : 0.516 7.498 12920 Z= 0.271 Chirality : 0.041 0.173 1404 Planarity : 0.004 0.031 1541 Dihedral : 16.248 153.961 1700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.89 % Allowed : 6.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1112 helix: 1.95 (0.18), residues: 823 sheet: 1.73 (1.28), residues: 20 loop : -0.75 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.028 0.001 PHE L 350 TYR 0.022 0.002 TYR M 113 ARG 0.002 0.000 ARG L 75 *********************** 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 102 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.040 Fit side-chains REVERT: M 1 MET cc_start: 0.5058 (tmm) cc_final: 0.4443 (mpp) REVERT: M 79 MET cc_start: 0.9133 (mtt) cc_final: 0.8638 (mtp) REVERT: M 105 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: M 141 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5149 (mm-30) REVERT: M 157 LYS cc_start: 0.8733 (mppt) cc_final: 0.8253 (mptt) REVERT: L 208 GLN cc_start: 0.7840 (mm110) cc_final: 0.7152 (mm-40) REVERT: L 365 MET cc_start: 0.8873 (mmm) cc_final: 0.8523 (mmm) REVERT: L 368 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: L 414 ASP cc_start: 0.8471 (m-30) cc_final: 0.7947 (t0) outliers start: 17 outliers final: 3 residues processed: 95 average time/residue: 1.9290 time to fit residues: 194.4440 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.078204 restraints weight = 12757.330| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.26 r_work: 0.2811 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9571 Z= 0.174 Angle : 0.513 5.984 12920 Z= 0.271 Chirality : 0.041 0.175 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.987 153.854 1700 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.45 % Allowed : 7.24 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1112 helix: 2.00 (0.18), residues: 817 sheet: 1.84 (1.29), residues: 20 loop : -0.67 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.027 0.001 PHE L 350 TYR 0.021 0.002 TYR M 433 ARG 0.002 0.000 ARG L 455 *********************** 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 103 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.936 Fit side-chains REVERT: M 1 MET cc_start: 0.5103 (tmm) cc_final: 0.4588 (mpp) REVERT: M 79 MET cc_start: 0.9097 (mtt) cc_final: 0.8703 (mtp) REVERT: M 105 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: M 141 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.4950 (mm-30) REVERT: M 157 LYS cc_start: 0.8737 (mppt) cc_final: 0.8264 (mptt) REVERT: L 208 GLN cc_start: 0.7839 (mm110) cc_final: 0.7162 (mm-40) REVERT: L 368 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: L 414 ASP cc_start: 0.8489 (m-30) cc_final: 0.7956 (t0) outliers start: 13 outliers final: 3 residues processed: 97 average time/residue: 1.6290 time to fit residues: 167.6416 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 : 0.910 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.078083 restraints weight = 12731.482| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.26 r_work: 0.2809 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2469 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= 0.179 Angle : 0.513 5.573 12920 Z= 0.271 Chirality : 0.041 0.176 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.808 153.707 1700 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.45 % Allowed : 8.13 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1112 helix: 1.95 (0.18), residues: 824 sheet: 1.81 (1.28), residues: 20 loop : -0.72 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 145 HIS 0.004 0.001 HIS L 245 PHE 0.027 0.001 PHE L 350 TYR 0.020 0.002 TYR M 433 ARG 0.001 0.000 ARG L 55 *********************** 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 97 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.918 Fit side-chains REVERT: M 1 MET cc_start: 0.5082 (tmm) cc_final: 0.4593 (mpp) REVERT: M 105 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: M 141 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.4952 (mm-30) REVERT: M 157 LYS cc_start: 0.8732 (mppt) cc_final: 0.8265 (mptt) REVERT: L 208 GLN cc_start: 0.7838 (mm110) cc_final: 0.7159 (mm-40) REVERT: L 368 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8140 (tm-30) outliers start: 13 outliers final: 4 residues processed: 90 average time/residue: 1.6511 time to fit residues: 157.8326 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 : 0.970 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.090152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077342 restraints weight = 12854.408| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.26 r_work: 0.2796 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9571 Z= 0.194 Angle : 0.523 5.582 12920 Z= 0.276 Chirality : 0.041 0.180 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.803 153.449 1700 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.34 % Allowed : 8.46 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1112 helix: 1.91 (0.18), residues: 824 sheet: 1.85 (1.29), residues: 20 loop : -0.72 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 363 PHE 0.027 0.001 PHE L 350 TYR 0.023 0.002 TYR L 426 ARG 0.001 0.000 ARG L 55 *********************** 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 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.987 Fit side-chains REVERT: M 1 MET cc_start: 0.5053 (tmm) cc_final: 0.4598 (mpp) REVERT: M 105 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: M 141 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.4838 (mm-30) REVERT: M 157 LYS cc_start: 0.8752 (mppt) cc_final: 0.8291 (mptt) REVERT: L 208 GLN cc_start: 0.7849 (mm110) cc_final: 0.7149 (mm-40) REVERT: L 368 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: L 414 ASP cc_start: 0.8500 (m-30) cc_final: 0.7907 (t0) outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 1.4895 time to fit residues: 140.9082 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 M residue 370 ASP 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 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 86 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.0060 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.078100 restraints weight = 12984.421| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.27 r_work: 0.2811 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9571 Z= 0.173 Angle : 0.510 5.545 12920 Z= 0.269 Chirality : 0.041 0.176 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.663 153.461 1700 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.45 % Allowed : 8.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1112 helix: 1.96 (0.18), residues: 824 sheet: 1.84 (1.30), residues: 20 loop : -0.69 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.004 0.001 HIS L 245 PHE 0.027 0.001 PHE L 350 TYR 0.021 0.002 TYR L 426 ARG 0.001 0.000 ARG L 75 *********************** 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 96 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.005 Fit side-chains REVERT: M 1 MET cc_start: 0.5100 (tmm) cc_final: 0.4679 (mpp) REVERT: M 105 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: M 141 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.4808 (mm-30) REVERT: M 157 LYS cc_start: 0.8735 (mppt) cc_final: 0.8264 (mptt) REVERT: M 309 MET cc_start: 0.7898 (ptm) cc_final: 0.7635 (ptm) REVERT: L 26 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8520 (ttpp) REVERT: L 208 GLN cc_start: 0.7836 (mm110) cc_final: 0.7158 (mm-40) REVERT: L 368 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8147 (tm-30) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 1.5683 time to fit residues: 153.1181 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.079309 restraints weight = 12845.632| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.27 r_work: 0.2831 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2635 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= 0.157 Angle : 0.498 5.531 12920 Z= 0.263 Chirality : 0.040 0.173 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.376 153.359 1700 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.34 % Allowed : 9.13 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1112 helix: 2.08 (0.18), residues: 814 sheet: 1.84 (1.30), residues: 20 loop : -0.47 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 PHE 0.028 0.001 PHE L 350 TYR 0.022 0.002 TYR M 433 ARG 0.001 0.000 ARG L 75 *********************** 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 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.998 Fit side-chains REVERT: M 1 MET cc_start: 0.5201 (tmm) cc_final: 0.4738 (mpp) REVERT: M 105 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: M 141 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.4774 (mm-30) REVERT: M 157 LYS cc_start: 0.8730 (mppt) cc_final: 0.8249 (mptt) REVERT: L 26 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: L 208 GLN cc_start: 0.7836 (mm110) cc_final: 0.7163 (mm-40) REVERT: L 368 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: L 414 ASP cc_start: 0.8454 (m-30) cc_final: 0.7832 (t0) outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 1.5328 time to fit residues: 148.1481 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.6980 chunk 110 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079753 restraints weight = 13026.220| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.20 r_work: 0.2855 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2600 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= 0.180 Angle : 0.517 5.563 12920 Z= 0.273 Chirality : 0.041 0.176 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.396 153.040 1700 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.34 % Allowed : 8.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1112 helix: 1.94 (0.18), residues: 829 sheet: 1.84 (1.30), residues: 20 loop : -0.68 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 PHE 0.027 0.001 PHE L 350 TYR 0.024 0.002 TYR L 426 ARG 0.001 0.000 ARG L 75 ********************** 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 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.989 Fit side-chains REVERT: M 1 MET cc_start: 0.5438 (tmm) cc_final: 0.4891 (mpp) REVERT: M 105 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: M 141 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.4906 (mm-30) REVERT: M 157 LYS cc_start: 0.8697 (mppt) cc_final: 0.8296 (mptt) REVERT: L 26 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (ttpp) REVERT: L 208 GLN cc_start: 0.7857 (mm110) cc_final: 0.7216 (mm-40) REVERT: L 368 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (tm-30) outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 1.5748 time to fit residues: 153.9651 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 621 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.079514 restraints weight = 13016.762| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.23 r_work: 0.2854 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2624 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= 0.176 Angle : 0.512 5.554 12920 Z= 0.271 Chirality : 0.041 0.177 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.289 153.132 1700 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.22 % Allowed : 9.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.25), residues: 1112 helix: 1.94 (0.18), residues: 830 sheet: 1.84 (1.30), residues: 20 loop : -0.65 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 145 HIS 0.005 0.001 HIS L 458 PHE 0.027 0.001 PHE L 350 TYR 0.023 0.002 TYR L 426 ARG 0.001 0.000 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7965.50 seconds wall clock time: 141 minutes 2.98 seconds (8462.98 seconds total)