Starting phenix.real_space_refine on Sat Aug 3 10:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwc_42661/08_2024/8uwc_42661_trim.cif" } resolution = 2.27 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= 0.018 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2459 2.51 5 N 655 2.21 5 O 816 1.98 5 H 3821 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A ARG 125": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 241": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 399": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 452": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A ARG 470": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 527": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 546": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7767 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7656 Classifications: {'peptide': 494} Link IDs: {'PCIS': 5, 'PTRANS': 22, 'TRANS': 466} Chain breaks: 4 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 111 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 97} Link IDs: {None: 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.66 Number of scatterers: 7767 At special positions: 0 Unit cell: (69.372, 84.87, 90.774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 816 8.00 N 655 7.00 C 2459 6.00 H 3821 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 501 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1101 " - " ASN A 515 " Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 939.9 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 7 sheets defined 29.4% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.506A pdb=" N GLY A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.916A pdb=" N LEU A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 412 through 431 removed outlier: 4.032A pdb=" N ALA A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.556A pdb=" N GLN A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.958A pdb=" N GLN A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 4.714A pdb=" N TYR A 54 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N VAL A 51 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N PHE A 133 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU A 53 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N LYS A 131 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 55 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 removed outlier: 7.479A pdb=" N ILE A 274 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 214 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 275 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 216 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG A 213 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN A 305 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 215 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 304 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA A 335 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU A 306 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 391 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 401 Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 485 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.737A pdb=" N ASP A 533 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 167 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3821 1.04 - 1.23: 392 1.23 - 1.43: 1283 1.43 - 1.63: 2234 1.63 - 1.83: 28 Bond restraints: 7758 Sorted by residual: bond pdb=" CA ASN A 91 " pdb=" CB ASN A 91 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.75e-02 3.27e+03 5.78e+00 bond pdb=" CB CYS A 407 " pdb=" SG CYS A 407 " ideal model delta sigma weight residual 1.808 1.746 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.47e+00 bond pdb=" N THR A 42 " pdb=" CA THR A 42 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 ... (remaining 7753 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.00: 219 107.00 - 113.76: 9239 113.76 - 120.53: 2422 120.53 - 127.29: 2092 127.29 - 134.06: 50 Bond angle restraints: 14022 Sorted by residual: angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" C VAL A 45 " ideal model delta sigma weight residual 106.53 110.77 -4.24 1.41e+00 5.03e-01 9.04e+00 angle pdb=" C LEU A 298 " pdb=" N LYS A 299 " pdb=" CA LYS A 299 " ideal model delta sigma weight residual 120.31 124.83 -4.52 1.52e+00 4.33e-01 8.85e+00 angle pdb=" C ILE A 123 " pdb=" N LYS A 124 " pdb=" CA LYS A 124 " ideal model delta sigma weight residual 120.44 124.29 -3.85 1.36e+00 5.41e-01 8.00e+00 angle pdb=" CA TYR A 561 " pdb=" CB TYR A 561 " pdb=" CG TYR A 561 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 7.00e+00 angle pdb=" CG ARG A 408 " pdb=" CD ARG A 408 " pdb=" NE ARG A 408 " ideal model delta sigma weight residual 112.00 116.81 -4.81 2.20e+00 2.07e-01 4.78e+00 ... (remaining 14017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3270 17.96 - 35.92: 268 35.92 - 53.88: 106 53.88 - 71.84: 32 71.84 - 89.80: 10 Dihedral angle restraints: 3686 sinusoidal: 2010 harmonic: 1676 Sorted by residual: dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 160.98 -67.98 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CA SER A 550 " pdb=" C SER A 550 " pdb=" N TYR A 551 " pdb=" CA TYR A 551 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N ILE A 528 " pdb=" CA ILE A 528 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 3683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 307 0.034 - 0.069: 167 0.069 - 0.103: 87 0.103 - 0.137: 40 0.137 - 0.172: 3 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB THR A 286 " pdb=" CA THR A 286 " pdb=" OG1 THR A 286 " pdb=" CG2 THR A 286 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A 106 " pdb=" N ILE A 106 " pdb=" C ILE A 106 " pdb=" CB ILE A 106 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 601 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " -0.023 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 56 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 575 " 0.024 2.00e-02 2.50e+03 8.75e-03 3.06e+00 pdb=" CG TRP A 575 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 575 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 575 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 575 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 575 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 575 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 575 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 575 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 575 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 575 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 575 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 575 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 575 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 575 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 575 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 237 " 0.018 2.00e-02 2.50e+03 7.91e-03 2.50e+00 pdb=" CG TRP A 237 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 237 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 237 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 237 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 237 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 237 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 237 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 237 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 237 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 237 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 237 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 237 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 237 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 237 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 237 " 0.002 2.00e-02 2.50e+03 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 177 2.08 - 2.71: 13013 2.71 - 3.34: 23457 3.34 - 3.97: 31647 3.97 - 4.60: 48559 Nonbonded interactions: 116853 Sorted by model distance: nonbonded pdb=" HE2 HIS A 225 " pdb=" O GLY A 402 " model vdw 1.446 2.450 nonbonded pdb="HH22 ARG A 134 " pdb=" OD1 ASP A 218 " model vdw 1.477 2.450 nonbonded pdb=" OD1 ASP A 467 " pdb=" H ARG A 470 " model vdw 1.563 2.450 nonbonded pdb=" O ALA A 194 " pdb=" H ALA A 199 " model vdw 1.579 2.450 nonbonded pdb=" HH TYR A 56 " pdb=" OE1 GLN A 110 " model vdw 1.611 2.450 ... (remaining 116848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 31.800 Find NCS groups from input model: 0.060 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.008 0.062 3937 Z= 0.487 Angle : 0.882 6.657 5348 Z= 0.497 Chirality : 0.054 0.172 604 Planarity : 0.005 0.033 682 Dihedral : 15.703 89.798 1441 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.67 % Allowed : 14.59 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.36), residues: 484 helix: -0.50 (0.43), residues: 121 sheet: -0.41 (0.50), residues: 102 loop : -1.62 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 575 HIS 0.007 0.002 HIS A 225 PHE 0.015 0.003 PHE A 228 TYR 0.028 0.004 TYR A 56 ARG 0.010 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 2.0704 time to fit residues: 136.0607 Evaluate side-chains 48 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3937 Z= 0.229 Angle : 0.608 4.458 5348 Z= 0.321 Chirality : 0.049 0.152 604 Planarity : 0.004 0.030 682 Dihedral : 7.815 59.408 558 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.83 % Allowed : 16.75 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.92 (0.38), residues: 484 helix: 0.65 (0.47), residues: 125 sheet: -0.52 (0.47), residues: 117 loop : -1.31 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 237 HIS 0.007 0.002 HIS A 225 PHE 0.009 0.001 PHE A 293 TYR 0.015 0.002 TYR A 63 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 62 average time/residue: 2.4157 time to fit residues: 156.2000 Evaluate side-chains 48 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3937 Z= 0.206 Angle : 0.565 4.825 5348 Z= 0.295 Chirality : 0.048 0.142 604 Planarity : 0.004 0.039 682 Dihedral : 6.706 58.921 552 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 19.86 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.62 (0.38), residues: 484 helix: 1.00 (0.47), residues: 125 sheet: -0.17 (0.48), residues: 111 loop : -1.27 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.008 0.001 PHE A 549 TYR 0.012 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 2.2404 time to fit residues: 125.9233 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3937 Z= 0.224 Angle : 0.576 6.635 5348 Z= 0.298 Chirality : 0.047 0.142 604 Planarity : 0.004 0.034 682 Dihedral : 5.943 59.102 552 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.11 % Allowed : 19.38 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.54 (0.38), residues: 484 helix: 1.06 (0.47), residues: 125 sheet: -0.30 (0.45), residues: 121 loop : -1.14 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 237 HIS 0.009 0.001 HIS A 225 PHE 0.009 0.001 PHE A 549 TYR 0.009 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 1.7349 time to fit residues: 98.8339 Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3937 Z= 0.243 Angle : 0.587 8.026 5348 Z= 0.301 Chirality : 0.047 0.143 604 Planarity : 0.004 0.033 682 Dihedral : 5.728 59.063 552 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.59 % Allowed : 19.62 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.58 (0.38), residues: 484 helix: 1.05 (0.46), residues: 125 sheet: -0.37 (0.45), residues: 121 loop : -1.15 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 237 HIS 0.008 0.001 HIS A 225 PHE 0.009 0.001 PHE A 549 TYR 0.009 0.001 TYR A 537 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6252 (ptt) cc_final: 0.6042 (ptt) outliers start: 15 outliers final: 7 residues processed: 53 average time/residue: 1.7988 time to fit residues: 100.2839 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3937 Z= 0.334 Angle : 0.653 9.241 5348 Z= 0.337 Chirality : 0.049 0.156 604 Planarity : 0.005 0.033 682 Dihedral : 5.998 59.644 552 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.35 % Allowed : 19.14 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.78 (0.38), residues: 484 helix: 0.80 (0.46), residues: 125 sheet: -0.48 (0.46), residues: 121 loop : -1.23 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.011 0.002 HIS A 225 PHE 0.011 0.002 PHE A 549 TYR 0.011 0.002 TYR A 56 ARG 0.006 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 1.8419 time to fit residues: 106.3147 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3937 Z= 0.198 Angle : 0.588 9.386 5348 Z= 0.296 Chirality : 0.047 0.141 604 Planarity : 0.004 0.032 682 Dihedral : 5.637 59.036 552 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.63 % Allowed : 19.86 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.52 (0.38), residues: 484 helix: 1.13 (0.47), residues: 125 sheet: -0.41 (0.46), residues: 121 loop : -1.08 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 237 HIS 0.005 0.001 HIS A 225 PHE 0.006 0.001 PHE A 549 TYR 0.009 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 1.7711 time to fit residues: 93.3043 Evaluate side-chains 48 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3937 Z= 0.228 Angle : 0.601 9.510 5348 Z= 0.304 Chirality : 0.047 0.141 604 Planarity : 0.004 0.032 682 Dihedral : 5.595 59.387 552 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.63 % Allowed : 18.90 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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 (0.38), residues: 484 helix: 1.18 (0.47), residues: 125 sheet: -0.37 (0.46), residues: 119 loop : -1.04 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.006 0.001 HIS A 225 PHE 0.007 0.001 PHE A 549 TYR 0.011 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 1.8377 time to fit residues: 92.6786 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3937 Z= 0.214 Angle : 0.594 9.412 5348 Z= 0.299 Chirality : 0.047 0.139 604 Planarity : 0.004 0.031 682 Dihedral : 5.549 59.565 552 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.15 % Allowed : 19.38 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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: -0.38 (0.39), residues: 484 helix: 1.24 (0.47), residues: 125 sheet: -0.37 (0.46), residues: 119 loop : -0.96 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.006 0.001 HIS A 225 PHE 0.008 0.001 PHE A 549 TYR 0.009 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.770 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 1.8199 time to fit residues: 93.6544 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3937 Z= 0.197 Angle : 0.588 9.217 5348 Z= 0.295 Chirality : 0.046 0.138 604 Planarity : 0.004 0.031 682 Dihedral : 5.443 59.508 552 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.15 % Allowed : 19.62 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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 (0.39), residues: 484 helix: 1.31 (0.47), residues: 125 sheet: -0.35 (0.47), residues: 119 loop : -0.82 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.005 0.001 HIS A 225 PHE 0.006 0.001 PHE A 293 TYR 0.008 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.644 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 1.8148 time to fit residues: 91.5488 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127179 restraints weight = 19430.566| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.32 r_work: 0.3855 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3937 Z= 0.243 Angle : 0.626 10.086 5348 Z= 0.314 Chirality : 0.047 0.143 604 Planarity : 0.004 0.032 682 Dihedral : 5.624 59.704 552 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.91 % Allowed : 20.10 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % 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 (0.39), residues: 484 helix: 1.25 (0.47), residues: 125 sheet: -0.37 (0.47), residues: 119 loop : -0.90 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.009 0.001 PHE A 549 TYR 0.009 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.52 seconds wall clock time: 73 minutes 55.11 seconds (4435.11 seconds total)