Starting phenix.real_space_refine on Thu Nov 14 08:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_45728.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_45728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_45728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_45728.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9clp_45728/11_2024/9clp_45728.cif" } resolution = 3.43 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= 0.026 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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, 4 Unusual residues: {' CA': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.91, per 1000 atoms: 1.57 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: 1.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.67 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: 1.61 Time building geometry restraints manager: 1.54 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: 11.840 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.490 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.002 0.079 5142 Z= 0.172 Angle : 0.524 4.302 6973 Z= 0.306 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 (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: 0.28 (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 TRP 0.029 0.002 TRP H 96 HIS 0.011 0.001 HIS A 347 PHE 0.008 0.001 PHE A 273 TYR 0.011 0.001 TYR A 239 ARG 0.006 0.001 ARG H 66 *********************** 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 : 0.494 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: 0.1954 time to fit residues: 19.6971 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS A 526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5142 Z= 0.170 Angle : 0.516 4.624 6973 Z= 0.284 Chirality : 0.042 0.146 751 Planarity : 0.004 0.040 914 Dihedral : 4.122 18.791 718 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.73 % Allowed : 5.29 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.34), residues: 645 helix: 0.45 (0.55), residues: 100 sheet: 1.32 (0.46), residues: 132 loop : -0.02 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 96 HIS 0.003 0.001 HIS A 341 PHE 0.015 0.001 PHE A 362 TYR 0.016 0.001 TYR A 539 ARG 0.004 0.001 ARG A 457 *********************** 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 71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8354 (t0) cc_final: 0.8059 (t0) REVERT: L 32 TYR cc_start: 0.7498 (m-10) cc_final: 0.6870 (m-10) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.1722 time to fit residues: 15.9001 Evaluate side-chains 65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 477 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 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.0020 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5142 Z= 0.166 Angle : 0.494 4.440 6973 Z= 0.270 Chirality : 0.041 0.141 751 Planarity : 0.004 0.048 914 Dihedral : 4.115 16.021 718 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.46 % Allowed : 6.39 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.34), residues: 645 helix: 0.88 (0.59), residues: 89 sheet: 1.30 (0.45), residues: 138 loop : -0.07 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 96 HIS 0.003 0.001 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.015 0.001 TYR A 548 ARG 0.008 0.001 ARG A 286 *********************** 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 72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8387 (t0) cc_final: 0.8042 (t0) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.2269 time to fit residues: 19.3977 Evaluate side-chains 64 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.0970 chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 59 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5142 Z= 0.166 Angle : 0.485 4.447 6973 Z= 0.262 Chirality : 0.041 0.141 751 Planarity : 0.004 0.047 914 Dihedral : 4.048 15.137 718 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.09 % Allowed : 8.03 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.34), residues: 645 helix: 0.95 (0.60), residues: 88 sheet: 1.22 (0.45), residues: 138 loop : -0.13 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 96 HIS 0.003 0.001 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.017 0.001 TYR A 539 ARG 0.011 0.001 ARG A 286 *********************** 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 72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8419 (t0) cc_final: 0.8025 (t0) REVERT: A 559 ASP cc_start: 0.7063 (t70) cc_final: 0.6734 (t70) REVERT: L 32 TYR cc_start: 0.7658 (m-10) cc_final: 0.7002 (m-10) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.2470 time to fit residues: 21.0207 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 : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5142 Z= 0.150 Angle : 0.475 4.532 6973 Z= 0.255 Chirality : 0.040 0.137 751 Planarity : 0.004 0.049 914 Dihedral : 3.932 15.463 718 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.46 % Allowed : 9.12 % 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 (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: 0.34 (0.34), residues: 645 helix: 0.69 (0.59), residues: 94 sheet: 1.23 (0.45), residues: 137 loop : -0.20 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 96 HIS 0.003 0.000 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.012 0.001 TYR A 548 ARG 0.009 0.001 ARG A 286 *********************** 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 75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8420 (t0) cc_final: 0.8046 (t0) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.2015 time to fit residues: 17.7718 Evaluate side-chains 67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 95 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 56 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5142 Z= 0.184 Angle : 0.492 4.873 6973 Z= 0.263 Chirality : 0.041 0.142 751 Planarity : 0.004 0.054 914 Dihedral : 4.019 15.600 718 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.82 % Allowed : 8.76 % 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 (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: 0.29 (0.34), residues: 645 helix: 0.64 (0.58), residues: 94 sheet: 1.12 (0.45), residues: 137 loop : -0.19 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.006 0.001 PHE L 62 TYR 0.015 0.001 TYR A 539 ARG 0.014 0.001 ARG A 286 *********************** 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 73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8448 (t0) cc_final: 0.8081 (t0) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.2254 time to fit residues: 18.9691 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 407 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 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 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5142 Z= 0.159 Angle : 0.479 5.453 6973 Z= 0.254 Chirality : 0.040 0.141 751 Planarity : 0.004 0.054 914 Dihedral : 3.926 15.224 718 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.46 % Allowed : 9.12 % 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 (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: 0.28 (0.34), residues: 645 helix: 0.74 (0.58), residues: 94 sheet: 1.02 (0.46), residues: 138 loop : -0.20 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.013 0.001 TYR L 32 ARG 0.014 0.001 ARG A 286 *********************** 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 69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.7119 (ttm) cc_final: 0.6848 (ttm) REVERT: A 426 ASP cc_start: 0.8449 (t0) cc_final: 0.8101 (t0) REVERT: L 32 TYR cc_start: 0.7650 (m-10) cc_final: 0.6982 (m-10) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.1899 time to fit residues: 15.6365 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 : 0.525 ------------------------------------------------------------------------------- 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 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 ILE 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 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5142 Z= 0.179 Angle : 0.489 5.905 6973 Z= 0.260 Chirality : 0.040 0.142 751 Planarity : 0.004 0.046 914 Dihedral : 3.969 15.282 718 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.64 % Allowed : 9.12 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.34), residues: 645 helix: 0.80 (0.59), residues: 94 sheet: 1.00 (0.45), residues: 137 loop : -0.24 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.014 0.001 TYR A 539 ARG 0.012 0.001 ARG A 286 *********************** 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: 9 poor density : 62 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8448 (t0) cc_final: 0.8094 (t0) REVERT: L 32 TYR cc_start: 0.7714 (m-10) cc_final: 0.7032 (m-10) outliers start: 9 outliers final: 9 residues processed: 64 average time/residue: 0.2096 time to fit residues: 17.4060 Evaluate side-chains 67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5142 Z= 0.176 Angle : 0.491 5.618 6973 Z= 0.261 Chirality : 0.040 0.141 751 Planarity : 0.004 0.042 914 Dihedral : 3.965 15.164 718 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.82 % Allowed : 8.76 % 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 (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: 0.23 (0.34), residues: 645 helix: 0.79 (0.59), residues: 95 sheet: 0.98 (0.45), residues: 137 loop : -0.26 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.012 0.001 TYR A 548 ARG 0.010 0.001 ARG A 286 *********************** 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 70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8439 (t0) cc_final: 0.8111 (t0) REVERT: L 32 TYR cc_start: 0.7723 (m-10) cc_final: 0.7024 (m-10) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1809 time to fit residues: 15.2406 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 : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 40 optimal weight: 0.0270 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5142 Z= 0.135 Angle : 0.468 5.691 6973 Z= 0.247 Chirality : 0.039 0.137 751 Planarity : 0.004 0.039 914 Dihedral : 3.718 14.458 718 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.09 % Allowed : 9.31 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.34), residues: 645 helix: 0.88 (0.59), residues: 95 sheet: 1.08 (0.45), residues: 138 loop : -0.16 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.005 0.001 PHE A 273 TYR 0.010 0.001 TYR A 548 ARG 0.010 0.001 ARG A 286 ********************** 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 76 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.7733 (tpp) cc_final: 0.7459 (tpp) REVERT: A 426 ASP cc_start: 0.8405 (t0) cc_final: 0.8114 (t0) REVERT: L 32 TYR cc_start: 0.7592 (m-10) cc_final: 0.7024 (m-10) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.1787 time to fit residues: 16.5695 Evaluate side-chains 72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain H residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 overall best weight: 0.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127777 restraints weight = 9949.835| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.73 r_work: 0.3345 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5142 Z= 0.150 Angle : 0.472 5.739 6973 Z= 0.249 Chirality : 0.040 0.139 751 Planarity : 0.004 0.040 914 Dihedral : 3.738 14.467 718 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.09 % Allowed : 9.49 % 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 (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: 0.34 (0.34), residues: 645 helix: 0.89 (0.59), residues: 95 sheet: 1.00 (0.45), residues: 138 loop : -0.17 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 96 HIS 0.002 0.000 HIS A 341 PHE 0.006 0.001 PHE A 273 TYR 0.011 0.001 TYR A 548 ARG 0.009 0.001 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.63 seconds wall clock time: 43 minutes 23.47 seconds (2603.47 seconds total)