Starting phenix.real_space_refine on Thu Feb 13 22:11:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qc1_18325/02_2025/8qc1_18325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qc1_18325/02_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_18325/02_2025/8qc1_18325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qc1_18325/02_2025/8qc1_18325.map" model { file = "/net/cci-nas-00/data/ceres_data/8qc1_18325/02_2025/8qc1_18325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qc1_18325/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.45, per 1000 atoms: 0.26 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: 2.57 Conformation dependent library (CDL) restraints added in 1.6 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: 0.95 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: 2.92 Time building geometry restraints manager: 2.90 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: 32.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.600 ------------------------------------------------------------------------------- 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 : 0.935 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: 1.5941 time to fit residues: 154.0696 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 : 1.024 ------------------------------------------------------------------------------- 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 = 0.090451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077701 restraints weight = 12583.370| |-----------------------------------------------------------------------------| 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: 0.2698 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- 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 6.763 12920 Z= 0.301 Chirality : 0.042 0.170 1404 Planarity : 0.004 0.031 1541 Dihedral : 17.587 153.982 1700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.72 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 : 0.965 Fit side-chains REVERT: M 79 MET cc_start: 0.9164 (mtt) cc_final: 0.8758 (mtp) REVERT: M 141 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5402 (pp20) REVERT: L 26 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8618 (ttpp) REVERT: L 414 ASP cc_start: 0.8409 (m-30) cc_final: 0.7914 (t0) outliers start: 17 outliers final: 2 residues processed: 104 average time/residue: 1.5091 time to fit residues: 166.9356 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 : 1.051 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.088865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.076081 restraints weight = 12706.413| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.25 r_work: 0.2772 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2058 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= 0.225 Angle : 0.558 7.870 12920 Z= 0.296 Chirality : 0.043 0.177 1404 Planarity : 0.004 0.029 1541 Dihedral : 16.954 153.869 1700 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.78 % Allowed : 5.79 % Favored : 92.43 % 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: 1.71 (0.25), residues: 1112 helix: 1.73 (0.18), residues: 823 sheet: 1.57 (1.26), residues: 20 loop : -0.73 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 145 HIS 0.004 0.001 HIS L 363 PHE 0.026 0.002 PHE L 350 TYR 0.028 0.002 TYR M 113 ARG 0.002 0.000 ARG L 75 *********************** 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 103 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.940 Fit side-chains REVERT: M 141 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5181 (mm-30) REVERT: M 157 LYS cc_start: 0.8742 (mppt) cc_final: 0.8296 (mptt) REVERT: L 368 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: L 414 ASP cc_start: 0.8504 (m-30) cc_final: 0.7937 (t0) outliers start: 16 outliers final: 3 residues processed: 96 average time/residue: 1.5343 time to fit residues: 156.4553 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 : 1.024 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 368 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.090446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.077666 restraints weight = 12622.684| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.25 r_work: 0.2801 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2265 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= 0.182 Angle : 0.522 7.712 12920 Z= 0.276 Chirality : 0.041 0.175 1404 Planarity : 0.004 0.030 1541 Dihedral : 16.527 154.152 1700 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.23 % Allowed : 6.46 % 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: 1.84 (0.25), residues: 1112 helix: 1.84 (0.18), residues: 824 sheet: 1.74 (1.28), residues: 20 loop : -0.78 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 145 HIS 0.004 0.001 HIS L 245 PHE 0.029 0.001 PHE L 350 TYR 0.021 0.002 TYR L 441 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 109 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.900 Fit side-chains REVERT: M 1 MET cc_start: 0.5068 (tmm) cc_final: 0.4455 (mpp) REVERT: M 79 MET cc_start: 0.9051 (mtt) cc_final: 0.8829 (mtp) REVERT: M 105 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: M 141 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5103 (mm-30) REVERT: M 157 LYS cc_start: 0.8743 (mppt) cc_final: 0.8291 (mptt) REVERT: L 208 GLN cc_start: 0.7846 (mm110) cc_final: 0.7177 (mm-40) REVERT: L 368 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: L 414 ASP cc_start: 0.8488 (m-30) cc_final: 0.7944 (t0) outliers start: 20 outliers final: 4 residues processed: 101 average time/residue: 1.6223 time to fit residues: 173.6918 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 : 1.028 ------------------------------------------------------------------------------- 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 38 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 94 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.092130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079367 restraints weight = 12760.800| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.26 r_work: 0.2831 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2471 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= 0.151 Angle : 0.496 6.049 12920 Z= 0.262 Chirality : 0.040 0.170 1404 Planarity : 0.004 0.032 1541 Dihedral : 16.088 154.086 1700 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.56 % Allowed : 7.46 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.25), residues: 1112 helix: 2.06 (0.18), residues: 811 sheet: 1.81 (1.30), residues: 20 loop : -0.61 (0.39), residues: 281 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 0.022 0.002 TYR L 426 ARG 0.002 0.000 ARG L 55 *********************** 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: 14 poor density : 89 time to evaluate : 1.093 Fit side-chains REVERT: M 1 MET cc_start: 0.4992 (tmm) cc_final: 0.4434 (mpp) REVERT: M 105 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: M 141 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.4955 (mm-30) REVERT: M 157 LYS cc_start: 0.8739 (mppt) cc_final: 0.8265 (mptt) REVERT: L 208 GLN cc_start: 0.7830 (mm110) cc_final: 0.7156 (mm-40) REVERT: L 368 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: L 414 ASP cc_start: 0.8464 (m-30) cc_final: 0.7928 (t0) outliers start: 14 outliers final: 3 residues processed: 96 average time/residue: 1.6198 time to fit residues: 165.0140 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 : 1.090 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.077152 restraints weight = 12717.726| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.26 r_work: 0.2788 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2433 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= 0.197 Angle : 0.526 5.613 12920 Z= 0.277 Chirality : 0.042 0.180 1404 Planarity : 0.004 0.031 1541 Dihedral : 16.067 153.623 1700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.56 % Allowed : 8.13 % Favored : 90.31 % 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: 1.89 (0.25), residues: 1112 helix: 1.90 (0.18), residues: 823 sheet: 1.80 (1.28), residues: 20 loop : -0.81 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 145 HIS 0.004 0.001 HIS L 363 PHE 0.027 0.001 PHE L 350 TYR 0.019 0.002 TYR M 433 ARG 0.001 0.000 ARG L 372 *********************** 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: 14 poor density : 83 time to evaluate : 0.944 Fit side-chains REVERT: M 1 MET cc_start: 0.5109 (tmm) cc_final: 0.4591 (mpp) REVERT: M 105 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: M 141 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.4911 (mm-30) REVERT: M 157 LYS cc_start: 0.8750 (mppt) cc_final: 0.8282 (mptt) REVERT: L 208 GLN cc_start: 0.7848 (mm110) cc_final: 0.7145 (mm-40) REVERT: L 368 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: L 414 ASP cc_start: 0.8487 (m-30) cc_final: 0.7948 (t0) outliers start: 14 outliers final: 5 residues processed: 90 average time/residue: 1.5678 time to fit residues: 150.0267 Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 424 SER 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: 0.5980 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.092068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079291 restraints weight = 12852.289| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.27 r_work: 0.2827 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2577 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= 0.152 Angle : 0.493 5.515 12920 Z= 0.260 Chirality : 0.040 0.172 1404 Planarity : 0.004 0.032 1541 Dihedral : 15.706 153.862 1700 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 (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: 2.09 (0.25), residues: 1112 helix: 2.03 (0.18), residues: 818 sheet: 1.87 (1.30), residues: 20 loop : -0.62 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 145 HIS 0.004 0.001 HIS L 245 PHE 0.028 0.001 PHE L 350 TYR 0.021 0.002 TYR L 441 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: 11 poor density : 84 time to evaluate : 0.938 Fit side-chains REVERT: M 1 MET cc_start: 0.5062 (tmm) cc_final: 0.4576 (mpp) REVERT: M 105 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: M 141 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.4797 (mm-30) REVERT: M 157 LYS cc_start: 0.8730 (mppt) cc_final: 0.8254 (mptt) REVERT: L 26 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8511 (ttpp) REVERT: L 208 GLN cc_start: 0.7844 (mm110) cc_final: 0.7165 (mm-40) REVERT: L 368 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8131 (tm-30) outliers start: 11 outliers final: 3 residues processed: 90 average time/residue: 1.5763 time to fit residues: 150.5506 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 : 1.033 ------------------------------------------------------------------------------- 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 86 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 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 = 0.3121 r_free = 0.3121 target = 0.090901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.078085 restraints weight = 12986.884| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.28 r_work: 0.2809 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2552 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= 0.176 Angle : 0.511 5.607 12920 Z= 0.269 Chirality : 0.041 0.176 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.668 153.423 1700 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 2.04 (0.25), residues: 1112 helix: 2.00 (0.18), residues: 817 sheet: 1.84 (1.29), residues: 20 loop : -0.65 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 21 *********************** 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 94 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.037 Fit side-chains REVERT: M 1 MET cc_start: 0.5093 (tmm) cc_final: 0.4655 (mpp) REVERT: M 105 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: M 141 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.4797 (mm-30) REVERT: M 157 LYS cc_start: 0.8735 (mppt) cc_final: 0.8263 (mptt) REVERT: L 26 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (ttpp) REVERT: L 208 GLN cc_start: 0.7837 (mm110) cc_final: 0.7151 (mm-40) REVERT: L 368 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: L 414 ASP cc_start: 0.8509 (m-30) cc_final: 0.7909 (t0) outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 1.6502 time to fit residues: 159.3541 Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 14 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3153 r_free = 0.3153 target = 0.092918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.080174 restraints weight = 12837.871| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.27 r_work: 0.2848 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2690 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= 0.141 Angle : 0.486 5.509 12920 Z= 0.256 Chirality : 0.040 0.172 1404 Planarity : 0.004 0.032 1541 Dihedral : 15.370 153.600 1700 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 9.24 % 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: 2.23 (0.25), residues: 1112 helix: 2.11 (0.18), residues: 814 sheet: 1.86 (1.31), residues: 20 loop : -0.45 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.029 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: 10 poor density : 85 time to evaluate : 0.930 Fit side-chains REVERT: M 1 MET cc_start: 0.5143 (tmm) cc_final: 0.4705 (mpp) REVERT: M 105 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: M 141 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.4784 (mm-30) REVERT: M 157 LYS cc_start: 0.8719 (mppt) cc_final: 0.8237 (mptt) REVERT: L 26 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8514 (ttpp) REVERT: L 208 GLN cc_start: 0.7833 (mm110) cc_final: 0.7162 (mm-40) REVERT: L 414 ASP cc_start: 0.8473 (m-30) cc_final: 0.7869 (t0) outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 1.4986 time to fit residues: 146.6899 Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.092033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.079907 restraints weight = 13045.194| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.21 r_work: 0.2850 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2593 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= 0.191 Angle : 0.521 5.582 12920 Z= 0.275 Chirality : 0.041 0.177 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.480 153.189 1700 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.11 % Allowed : 9.24 % 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: 2.04 (0.25), residues: 1112 helix: 1.99 (0.18), residues: 817 sheet: 1.81 (1.28), residues: 20 loop : -0.63 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 145 HIS 0.004 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 M 76 ********************** 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 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.011 Fit side-chains REVERT: M 1 MET cc_start: 0.5330 (tmm) cc_final: 0.4797 (mpp) REVERT: M 105 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: M 141 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.4873 (mm-30) REVERT: M 157 LYS cc_start: 0.8695 (mppt) cc_final: 0.8296 (mptt) REVERT: M 177 MET cc_start: 0.9214 (ttp) cc_final: 0.8865 (ttp) REVERT: L 26 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8558 (ttpp) REVERT: L 208 GLN cc_start: 0.7868 (mm110) cc_final: 0.7214 (mm-40) REVERT: L 414 ASP cc_start: 0.8454 (m-30) cc_final: 0.7954 (t0) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 1.5777 time to fit residues: 146.0304 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 : 0.997 ------------------------------------------------------------------------------- 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 308 ASP 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 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: 4.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.092900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080837 restraints weight = 13026.492| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.21 r_work: 0.2869 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2661 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= 0.161 Angle : 0.504 5.534 12920 Z= 0.265 Chirality : 0.040 0.174 1404 Planarity : 0.004 0.031 1541 Dihedral : 15.303 153.354 1700 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.11 % Allowed : 9.24 % 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: 2.16 (0.25), residues: 1112 helix: 2.05 (0.18), residues: 814 sheet: 1.85 (1.30), residues: 20 loop : -0.47 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 145 HIS 0.004 0.001 HIS L 458 PHE 0.028 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: 6553.08 seconds wall clock time: 117 minutes 26.96 seconds (7046.96 seconds total)