Starting phenix.real_space_refine on Thu Jul 2 01:04:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/07_2026/9clp_45728.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 3 9.91 5 Zn 1 6.06 5 S 53 5.16 5 C 3127 2.51 5 N 864 2.21 5 O 987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5035 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3257 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 420, 3249 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 399} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 420, 3249 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 399} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3310 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 795 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 1 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Time building chain proxies: 1.48, per 1000 atoms: 0.29 Number of scatterers: 5035 At special positions: 0 Unit cell: (66.222, 70.75, 126.218, 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) Zn 1 29.99 Ca 3 19.99 S 53 16.00 O 987 8.00 N 864 7.00 C 3127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 451 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 609 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 302.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 347 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 341 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 337 " 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 21.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.764A pdb=" N TYR A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 265 through 285 removed outlier: 5.100A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.646A pdb=" N MET A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.040A pdb=" N GLY A 363 " --> pdb=" O ILE A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.851A pdb=" N TYR A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.572A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 394 " --> pdb=" O LYS A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.690A pdb=" N GLY A 563 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.768A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.769A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.715A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 253 removed outlier: 7.870A pdb=" N VAL A 207 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 251 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 209 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE A 253 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N HIS A 289 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A 204 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN A 291 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 206 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 293 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 208 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.529A pdb=" N ASP A 433 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 438 " --> pdb=" O ASP A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 464 removed outlier: 7.123A pdb=" N GLU A 474 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 605 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.525A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.872A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 24 152 hydrogen bonds defined for protein. 372 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: 0.70 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1672 1.35 - 1.46: 1241 1.46 - 1.58: 2162 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 5142 Sorted by residual: bond pdb=" CB PRO A 390 " pdb=" CG PRO A 390 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.47e+00 bond pdb=" N ASN L 31 " pdb=" CA ASN L 31 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.19e+00 bond pdb=" C VAL A 249 " pdb=" O VAL A 249 " ideal model delta sigma weight residual 1.231 1.243 -0.012 1.02e-02 9.61e+03 1.39e+00 bond pdb=" CA MET A 576 " pdb=" C MET A 576 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.63e-01 bond pdb=" CG PRO A 390 " pdb=" CD PRO A 390 " ideal model delta sigma weight residual 1.503 1.532 -0.029 3.40e-02 8.65e+02 7.09e-01 ... (remaining 5137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 6420 0.86 - 1.72: 438 1.72 - 2.58: 79 2.58 - 3.44: 26 3.44 - 4.30: 10 Bond angle restraints: 6973 Sorted by residual: angle pdb=" C ASP A 586 " pdb=" N GLU A 587 " pdb=" CA GLU A 587 " ideal model delta sigma weight residual 120.38 124.30 -3.92 1.37e+00 5.33e-01 8.20e+00 angle pdb=" CA PRO A 390 " pdb=" N PRO A 390 " pdb=" CD PRO A 390 " ideal model delta sigma weight residual 112.00 108.21 3.79 1.40e+00 5.10e-01 7.32e+00 angle pdb=" C GLU A 462 " pdb=" N CYS A 463 " pdb=" CA CYS A 463 " ideal model delta sigma weight residual 122.42 118.66 3.76 1.77e+00 3.19e-01 4.51e+00 angle pdb=" C TYR A 309 " pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " ideal model delta sigma weight residual 111.36 108.03 3.33 1.63e+00 3.76e-01 4.17e+00 angle pdb=" C VAL A 308 " pdb=" N TYR A 309 " pdb=" CA TYR A 309 " ideal model delta sigma weight residual 123.05 126.23 -3.18 1.57e+00 4.06e-01 4.11e+00 ... (remaining 6968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 2884 17.26 - 34.52: 180 34.52 - 51.78: 41 51.78 - 69.04: 9 69.04 - 86.30: 8 Dihedral angle restraints: 3122 sinusoidal: 1222 harmonic: 1900 Sorted by residual: dihedral pdb=" CB CYS A 463 " pdb=" SG CYS A 463 " pdb=" SG CYS A 483 " pdb=" CB CYS A 483 " ideal model delta sinusoidal sigma weight residual 93.00 178.90 -85.90 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual -86.00 -158.19 72.19 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 359 " pdb=" CB CYS A 359 " ideal model delta sinusoidal sigma weight residual -86.00 -150.72 64.72 1 1.00e+01 1.00e-02 5.50e+01 ... (remaining 3119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 433 0.026 - 0.053: 195 0.053 - 0.079: 71 0.079 - 0.106: 39 0.106 - 0.132: 13 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASN L 31 " pdb=" N ASN L 31 " pdb=" C ASN L 31 " pdb=" CB ASN L 31 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 748 not shown) Planarity restraints: 914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 389 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 390 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 96 " 0.012 2.00e-02 2.50e+03 1.06e-02 2.82e+00 pdb=" CG TRP H 96 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP H 96 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP H 96 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 96 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 96 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 96 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 96 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 96 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 357 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 358 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.021 5.00e-02 4.00e+02 ... (remaining 911 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 143 2.71 - 3.26: 5003 3.26 - 3.80: 7490 3.80 - 4.35: 9600 4.35 - 4.90: 16839 Nonbonded interactions: 39075 Sorted by model distance: nonbonded pdb=" CG HIS A 347 " pdb="ZN ZN A 701 " model vdw 2.160 1.960 nonbonded pdb=" OG1 THR A 306 " pdb=" O VAL A 318 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A 210 " pdb=" N HIS A 211 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" O GLY L 77 " model vdw 2.303 3.120 nonbonded pdb=" O VAL A 308 " pdb=" NH1 ARG A 316 " model vdw 2.309 3.120 ... (remaining 39070 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=0.50 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: 14.440 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.012 0.811 5164 Z= 0.394 Angle : 0.527 4.302 7011 Z= 0.307 Chirality : 0.040 0.132 751 Planarity : 0.005 0.068 914 Dihedral : 12.339 86.297 1855 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.33), residues: 645 helix: 0.48 (0.56), residues: 93 sheet: 1.05 (0.45), residues: 139 loop : -0.14 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.011 0.001 TYR A 239 PHE 0.008 0.001 PHE A 273 TRP 0.029 0.002 TRP H 96 HIS 0.011 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 5142) covalent geometry : angle 0.52403 / 0.31 ( 6973) SS BOND : bond 0.00187 / 0.12 ( 19) SS BOND : angle 0.89012 / 0.71 ( 38) hydrogen bonds : bond 0.21022 / 13.84 ( 148) hydrogen bonds : angle 7.08299 / 5.38 ( 372) metal coordination : bond 0.46839 / 23.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6870 (mm-30) REVERT: A 303 LEU cc_start: 0.8716 (mt) cc_final: 0.8502 (mt) REVERT: A 426 ASP cc_start: 0.8310 (t0) cc_final: 0.8095 (t0) REVERT: L 32 TYR cc_start: 0.7339 (m-10) cc_final: 0.6916 (m-10) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0802 time to fit residues: 8.2043 Evaluate side-chains 63 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS A 475 HIS A 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126402 restraints weight = 7983.463| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.06 r_work: 0.3237 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5164 Z= 0.146 Angle : 0.553 4.439 7011 Z= 0.303 Chirality : 0.043 0.148 751 Planarity : 0.005 0.042 914 Dihedral : 4.383 18.585 718 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.09 % Allowed : 5.29 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.34), residues: 645 helix: 0.35 (0.55), residues: 100 sheet: 1.17 (0.45), residues: 132 loop : -0.10 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.017 0.001 TYR A 548 PHE 0.016 0.002 PHE A 362 TRP 0.020 0.001 TRP H 96 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 5142) covalent geometry : angle 0.55055 / 0.30 ( 6973) SS BOND : bond 0.00351 / 0.23 ( 19) SS BOND : angle 0.84853 / 0.55 ( 38) hydrogen bonds : bond 0.04255 / 2.74 ( 148) hydrogen bonds : angle 5.26300 / 3.98 ( 372) metal coordination : bond 0.00571 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 426 ASP cc_start: 0.8715 (t0) cc_final: 0.8269 (t0) REVERT: A 467 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7894 (mtt90) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0726 time to fit residues: 6.7553 Evaluate side-chains 65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111101 restraints weight = 13342.361| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.94 r_work: 0.3097 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5164 Z= 0.227 Angle : 0.623 4.977 7011 Z= 0.339 Chirality : 0.046 0.147 751 Planarity : 0.005 0.052 914 Dihedral : 5.003 19.031 718 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.46 % Allowed : 7.30 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.33), residues: 645 helix: 0.48 (0.57), residues: 89 sheet: 0.75 (0.46), residues: 134 loop : -0.46 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.018 0.002 TYR A 548 PHE 0.012 0.002 PHE L 62 TRP 0.024 0.002 TRP H 96 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 ( 5142) covalent geometry : angle 0.62058 / 0.34 ( 6973) SS BOND : bond 0.00447 / 0.31 ( 19) SS BOND : angle 0.95498 / 0.61 ( 38) hydrogen bonds : bond 0.04652 / 2.98 ( 148) hydrogen bonds : angle 5.20198 / 3.90 ( 372) metal coordination : bond 0.00814 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 426 ASP cc_start: 0.8765 (t0) cc_final: 0.8368 (t0) REVERT: H 34 MET cc_start: 0.8371 (mmm) cc_final: 0.8081 (ttm) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.0752 time to fit residues: 6.5496 Evaluate side-chains 64 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124402 restraints weight = 12025.720| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.81 r_work: 0.3200 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5164 Z= 0.127 Angle : 0.515 5.248 7011 Z= 0.280 Chirality : 0.041 0.141 751 Planarity : 0.004 0.039 914 Dihedral : 4.536 16.677 718 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.28 % Allowed : 9.31 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.33), residues: 645 helix: 0.56 (0.58), residues: 90 sheet: 0.78 (0.44), residues: 137 loop : -0.40 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.019 0.001 TYR L 32 PHE 0.007 0.001 PHE A 273 TRP 0.017 0.001 TRP H 96 HIS 0.003 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5142) covalent geometry : angle 0.51381 / 0.28 ( 6973) SS BOND : bond 0.00310 / 0.20 ( 19) SS BOND : angle 0.75260 / 0.46 ( 38) hydrogen bonds : bond 0.03547 / 2.28 ( 148) hydrogen bonds : angle 4.85011 / 3.66 ( 372) metal coordination : bond 0.00334 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 426 ASP cc_start: 0.8796 (t0) cc_final: 0.8391 (t0) REVERT: A 539 TYR cc_start: 0.7666 (p90) cc_final: 0.7432 (p90) REVERT: A 559 ASP cc_start: 0.7117 (t70) cc_final: 0.6864 (t70) REVERT: H 34 MET cc_start: 0.8278 (mmm) cc_final: 0.7851 (ttm) REVERT: H 105 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7895 (pm20) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.0775 time to fit residues: 6.5937 Evaluate side-chains 62 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 chunk 55 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129979 restraints weight = 9283.841| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.79 r_work: 0.3375 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5164 Z= 0.087 Angle : 0.469 4.718 7011 Z= 0.253 Chirality : 0.039 0.132 751 Planarity : 0.004 0.049 914 Dihedral : 3.963 14.817 718 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.91 % Allowed : 10.77 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.33), residues: 645 helix: 0.68 (0.59), residues: 94 sheet: 0.83 (0.44), residues: 138 loop : -0.33 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 286 TYR 0.016 0.001 TYR L 32 PHE 0.005 0.001 PHE A 273 TRP 0.012 0.001 TRP H 96 HIS 0.003 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 5142) covalent geometry : angle 0.46845 / 0.25 ( 6973) SS BOND : bond 0.00190 / 0.12 ( 19) SS BOND : angle 0.55323 / 0.34 ( 38) hydrogen bonds : bond 0.02803 / 1.83 ( 148) hydrogen bonds : angle 4.53483 / 3.45 ( 372) metal coordination : bond 0.00097 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.7936 (tpt) cc_final: 0.7693 (tpp) REVERT: A 252 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 426 ASP cc_start: 0.8796 (t0) cc_final: 0.8332 (t0) REVERT: A 539 TYR cc_start: 0.7490 (p90) cc_final: 0.7183 (p90) REVERT: H 7 SER cc_start: 0.8509 (p) cc_final: 0.8221 (t) REVERT: L 32 TYR cc_start: 0.7753 (m-10) cc_final: 0.7178 (m-80) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.0897 time to fit residues: 8.1821 Evaluate side-chains 67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.2980 chunk 59 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.0170 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129991 restraints weight = 6108.750| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.68 r_work: 0.3408 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5164 Z= 0.092 Angle : 0.476 5.425 7011 Z= 0.254 Chirality : 0.040 0.143 751 Planarity : 0.004 0.053 914 Dihedral : 3.883 15.503 718 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.09 % Allowed : 10.58 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.33), residues: 645 helix: 1.16 (0.59), residues: 88 sheet: 0.90 (0.44), residues: 138 loop : -0.31 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 286 TYR 0.012 0.001 TYR A 548 PHE 0.006 0.001 PHE A 273 TRP 0.010 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 5142) covalent geometry : angle 0.47583 / 0.25 ( 6973) SS BOND : bond 0.00201 / 0.13 ( 19) SS BOND : angle 0.50423 / 0.32 ( 38) hydrogen bonds : bond 0.02894 / 1.83 ( 148) hydrogen bonds : angle 4.48422 / 3.42 ( 372) metal coordination : bond 0.00175 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 213 MET cc_start: 0.7903 (tpt) cc_final: 0.7545 (tpp) REVERT: A 252 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 426 ASP cc_start: 0.8798 (t0) cc_final: 0.8335 (t0) REVERT: A 539 TYR cc_start: 0.7509 (p90) cc_final: 0.7179 (p90) REVERT: L 32 TYR cc_start: 0.7750 (m-10) cc_final: 0.7212 (m-10) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.0760 time to fit residues: 6.2683 Evaluate side-chains 63 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126496 restraints weight = 12112.110| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.83 r_work: 0.3330 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5164 Z= 0.114 Angle : 0.498 5.070 7011 Z= 0.265 Chirality : 0.040 0.142 751 Planarity : 0.004 0.056 914 Dihedral : 4.001 15.439 718 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 9.67 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.33), residues: 645 helix: 1.12 (0.59), residues: 88 sheet: 0.90 (0.45), residues: 137 loop : -0.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 286 TYR 0.012 0.001 TYR A 548 PHE 0.006 0.001 PHE A 273 TRP 0.009 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 5142) covalent geometry : angle 0.49785 / 0.26 ( 6973) SS BOND : bond 0.00250 / 0.17 ( 19) SS BOND : angle 0.56659 / 0.35 ( 38) hydrogen bonds : bond 0.03214 / 2.06 ( 148) hydrogen bonds : angle 4.48891 / 3.40 ( 372) metal coordination : bond 0.00360 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.7960 (tpt) cc_final: 0.7614 (tpp) REVERT: A 252 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 311 MET cc_start: 0.8034 (tpp) cc_final: 0.7663 (tpp) REVERT: A 426 ASP cc_start: 0.8816 (t0) cc_final: 0.8360 (t0) REVERT: A 539 TYR cc_start: 0.7550 (p90) cc_final: 0.7197 (p90) REVERT: H 105 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: L 32 TYR cc_start: 0.7864 (m-10) cc_final: 0.7255 (m-10) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0768 time to fit residues: 6.3185 Evaluate side-chains 68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 55 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116130 restraints weight = 8021.752| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.08 r_work: 0.3328 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5164 Z= 0.118 Angle : 0.504 6.191 7011 Z= 0.267 Chirality : 0.041 0.143 751 Planarity : 0.004 0.040 914 Dihedral : 4.072 15.694 718 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.82 % Allowed : 10.58 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.33), residues: 645 helix: 1.12 (0.60), residues: 88 sheet: 0.79 (0.45), residues: 138 loop : -0.39 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 286 TYR 0.011 0.001 TYR A 548 PHE 0.006 0.001 PHE A 273 TRP 0.010 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 5142) covalent geometry : angle 0.50381 / 0.27 ( 6973) SS BOND : bond 0.00252 / 0.17 ( 19) SS BOND : angle 0.57932 / 0.36 ( 38) hydrogen bonds : bond 0.03252 / 2.07 ( 148) hydrogen bonds : angle 4.48291 / 3.39 ( 372) metal coordination : bond 0.00389 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.7900 (tpt) cc_final: 0.7551 (tpp) REVERT: A 252 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 426 ASP cc_start: 0.8837 (t0) cc_final: 0.8387 (t0) REVERT: A 539 TYR cc_start: 0.7513 (p90) cc_final: 0.7189 (p90) REVERT: H 105 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: L 32 TYR cc_start: 0.7886 (m-10) cc_final: 0.7237 (m-10) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.0874 time to fit residues: 7.1850 Evaluate side-chains 66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115027 restraints weight = 6101.750| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.56 r_work: 0.3344 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5164 Z= 0.171 Angle : 0.554 5.404 7011 Z= 0.295 Chirality : 0.042 0.145 751 Planarity : 0.004 0.044 914 Dihedral : 4.369 16.078 718 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.82 % Allowed : 9.85 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.33), residues: 645 helix: 0.95 (0.59), residues: 89 sheet: 0.58 (0.44), residues: 136 loop : -0.54 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.014 0.002 TYR H 91 PHE 0.007 0.001 PHE A 530 TRP 0.011 0.001 TRP H 96 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5142) covalent geometry : angle 0.55282 / 0.29 ( 6973) SS BOND : bond 0.00353 / 0.25 ( 19) SS BOND : angle 0.74531 / 0.46 ( 38) hydrogen bonds : bond 0.03818 / 2.42 ( 148) hydrogen bonds : angle 4.67101 / 3.52 ( 372) metal coordination : bond 0.00689 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 426 ASP cc_start: 0.8837 (t0) cc_final: 0.8402 (t0) REVERT: A 539 TYR cc_start: 0.7539 (p90) cc_final: 0.7261 (p90) REVERT: A 559 ASP cc_start: 0.7210 (t70) cc_final: 0.6736 (t70) REVERT: H 105 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7940 (pm20) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0827 time to fit residues: 6.9757 Evaluate side-chains 66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115320 restraints weight = 9753.500| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.37 r_work: 0.3293 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5164 Z= 0.133 Angle : 0.529 5.604 7011 Z= 0.282 Chirality : 0.041 0.141 751 Planarity : 0.004 0.039 914 Dihedral : 4.275 15.974 718 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.64 % Allowed : 10.04 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.33), residues: 645 helix: 1.05 (0.60), residues: 88 sheet: 0.47 (0.44), residues: 137 loop : -0.53 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.037 0.001 TYR L 32 PHE 0.007 0.001 PHE A 273 TRP 0.012 0.001 TRP H 96 HIS 0.003 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 5142) covalent geometry : angle 0.52826 / 0.28 ( 6973) SS BOND : bond 0.00284 / 0.19 ( 19) SS BOND : angle 0.65894 / 0.40 ( 38) hydrogen bonds : bond 0.03464 / 2.19 ( 148) hydrogen bonds : angle 4.60094 / 3.48 ( 372) metal coordination : bond 0.00450 / 0.23 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.7939 (tpt) cc_final: 0.7587 (tpp) REVERT: A 252 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 338 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 426 ASP cc_start: 0.8870 (t0) cc_final: 0.8421 (t0) REVERT: A 539 TYR cc_start: 0.7530 (p90) cc_final: 0.7194 (p90) REVERT: H 105 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7964 (pm20) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.0732 time to fit residues: 6.5406 Evaluate side-chains 70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121787 restraints weight = 7984.748| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.10 r_work: 0.3326 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5164 Z= 0.130 Angle : 0.528 5.713 7011 Z= 0.280 Chirality : 0.041 0.142 751 Planarity : 0.004 0.039 914 Dihedral : 4.242 15.822 718 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.01 % Allowed : 10.22 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.33), residues: 645 helix: 1.07 (0.60), residues: 88 sheet: 0.46 (0.44), residues: 137 loop : -0.52 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.022 0.001 TYR L 32 PHE 0.007 0.001 PHE A 273 TRP 0.011 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5142) covalent geometry : angle 0.52721 / 0.28 ( 6973) SS BOND : bond 0.00274 / 0.19 ( 19) SS BOND : angle 0.63130 / 0.38 ( 38) hydrogen bonds : bond 0.03411 / 2.16 ( 148) hydrogen bonds : angle 4.59338 / 3.48 ( 372) metal coordination : bond 0.00455 / 0.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.35 seconds wall clock time: 28 minutes 50.82 seconds (1730.82 seconds total)