Starting phenix.real_space_refine on Wed Feb 14 02:28:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/02_2024/8d2x_27153_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1611 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4465 2.51 5 N 1027 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6813 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Conformer: "B" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1401 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1416 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1433 Chain: "A" Number of atoms: 551 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 417 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N AMET A 181 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 181 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 604 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 604 " occ=0.50 residue: pdb=" C1 ALMT A 613 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 613 " occ=0.50 Time building chain proxies: 6.42, per 1000 atoms: 0.94 Number of scatterers: 6813 At special positions: 0 Unit cell: (70.896, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1288 8.00 N 1027 7.00 C 4465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.02 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 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 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 2.1 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 10 sheets defined 42.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.658A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.654A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 88 " --> pdb=" O AARG A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 110 through 127 Proline residue: A 118 - end of helix removed outlier: 3.519A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 158 - end of helix removed outlier: 3.527A pdb=" N ALA A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 276 through 287 removed outlier: 4.258A pdb=" N PHE A 279 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 318 removed outlier: 4.939A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.568A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.333A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 420 through 450 Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.663A pdb=" N LEU A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 494 through 506 removed outlier: 5.105A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 Processing sheet with id= B, first strand: chain 'B' and resid 83 through 88 removed outlier: 5.978A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 140 through 145 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.544A pdb=" N ALA C 77 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.857A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= H, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.867A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.744A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.726A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 964 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: 2.01 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 990 1.31 - 1.44: 1961 1.44 - 1.56: 3948 1.56 - 1.69: 55 1.69 - 1.81: 46 Bond restraints: 7000 Sorted by residual: bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.523 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C1B LMT A 610 " pdb=" O5B LMT A 610 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C1B LMT A 608 " pdb=" O5B LMT A 608 " ideal model delta sigma weight residual 1.393 1.520 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1BALMT A 613 " pdb=" O5BALMT A 613 " ideal model delta sigma weight residual 1.393 1.518 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 99.13 - 109.74: 1213 109.74 - 120.36: 5543 120.36 - 130.97: 2755 130.97 - 141.59: 34 141.59 - 152.20: 3 Bond angle restraints: 9548 Sorted by residual: angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 130.46 -20.96 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C ALA C 193 " pdb=" CA ALA C 193 " pdb=" CB ALA C 193 " ideal model delta sigma weight residual 115.89 110.32 5.57 1.32e+00 5.74e-01 1.78e+01 angle pdb=" C ILE A 211 " pdb=" CA ILE A 211 " pdb=" CB ILE A 211 " ideal model delta sigma weight residual 112.04 107.67 4.37 1.31e+00 5.83e-01 1.11e+01 angle pdb=" C ARG A 455 " pdb=" N GLY A 456 " pdb=" CA GLY A 456 " ideal model delta sigma weight residual 121.41 115.05 6.36 1.96e+00 2.60e-01 1.05e+01 angle pdb=" C GLY B 180 " pdb=" N PRO B 181 " pdb=" CA PRO B 181 " ideal model delta sigma weight residual 121.00 117.28 3.72 1.16e+00 7.43e-01 1.03e+01 ... (remaining 9543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 4071 26.29 - 52.58: 254 52.58 - 78.87: 105 78.87 - 105.16: 101 105.16 - 131.45: 79 Dihedral angle restraints: 4610 sinusoidal: 2138 harmonic: 2472 Sorted by residual: dihedral pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " pdb=" C09 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 77.11 -151.44 -131.45 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1' LMT A 608 " pdb=" C2' LMT A 608 " pdb=" C3' LMT A 608 " pdb=" O3' LMT A 608 " ideal model delta sinusoidal sigma weight residual -176.68 -60.58 -116.10 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2B LMT A 611 " pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " pdb=" C5B LMT A 611 " ideal model delta sinusoidal sigma weight residual -57.12 58.43 -115.55 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 837 0.053 - 0.107: 230 0.107 - 0.160: 73 0.160 - 0.213: 7 0.213 - 0.266: 8 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1B LMT A 605 " pdb=" C2B LMT A 605 " pdb=" O1B LMT A 605 " pdb=" O5B LMT A 605 " both_signs ideal model delta sigma weight residual False -2.20 -2.47 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' LMT A 614 " pdb=" C3' LMT A 614 " pdb=" C5' LMT A 614 " pdb=" O1B LMT A 614 " both_signs ideal model delta sigma weight residual False -2.55 -2.29 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.45 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1152 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 204 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ALA A 204 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 204 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 205 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 47 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1544 2.79 - 3.32: 6003 3.32 - 3.84: 11589 3.84 - 4.37: 12613 4.37 - 4.90: 22720 Nonbonded interactions: 54469 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLN A 152 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.308 2.440 nonbonded pdb=" O SER B 30 " pdb=" OG SER B 30 " model vdw 2.343 2.440 nonbonded pdb=" O THR A 381 " pdb=" OG SER A 385 " model vdw 2.344 2.440 ... (remaining 54464 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=0.50 max=1.00 mean=0.98 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 11.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.140 Find NCS groups from input model: 0.180 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.130 7000 Z= 0.752 Angle : 1.290 20.964 9548 Z= 0.538 Chirality : 0.057 0.266 1155 Planarity : 0.007 0.054 1135 Dihedral : 30.615 131.450 3024 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.22 % Rotamer: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.26), residues: 871 helix: 0.18 (0.24), residues: 390 sheet: -0.79 (0.40), residues: 162 loop : -3.13 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 106 HIS 0.002 0.001 HIS A 156 PHE 0.021 0.002 PHE B 89 TYR 0.016 0.001 TYR B 48 ARG 0.002 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.666 Fit side-chains REVERT: A 70 LEU cc_start: 0.8582 (mt) cc_final: 0.8381 (mt) REVERT: A 134 ASP cc_start: 0.7768 (m-30) cc_final: 0.7261 (p0) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1904 time to fit residues: 39.5209 Evaluate side-chains 117 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 311 ASN A 324 ASN A 345 GLN B 23 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 57 GLN C 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7000 Z= 0.273 Angle : 0.903 9.178 9548 Z= 0.382 Chirality : 0.055 0.495 1155 Planarity : 0.005 0.055 1135 Dihedral : 18.924 70.913 1848 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.89 % Allowed : 12.67 % Favored : 83.45 % 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: -1.03 (0.27), residues: 871 helix: 1.13 (0.25), residues: 386 sheet: -0.72 (0.42), residues: 158 loop : -3.01 (0.28), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 103 HIS 0.004 0.002 HIS A 288 PHE 0.016 0.002 PHE B 89 TYR 0.016 0.001 TYR A 251 ARG 0.004 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.685 Fit side-chains REVERT: A 134 ASP cc_start: 0.7729 (m-30) cc_final: 0.7281 (p0) REVERT: A 291 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6241 (t80) outliers start: 22 outliers final: 15 residues processed: 137 average time/residue: 0.1814 time to fit residues: 33.4835 Evaluate side-chains 129 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7000 Z= 0.238 Angle : 0.779 9.185 9548 Z= 0.343 Chirality : 0.048 0.318 1155 Planarity : 0.005 0.053 1135 Dihedral : 12.382 59.143 1848 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.87 % Allowed : 17.23 % Favored : 79.90 % 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: -0.85 (0.28), residues: 871 helix: 1.39 (0.25), residues: 386 sheet: -0.91 (0.40), residues: 163 loop : -2.93 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 103 HIS 0.003 0.001 HIS A 288 PHE 0.016 0.002 PHE C 38 TYR 0.015 0.001 TYR A 251 ARG 0.004 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.690 Fit side-chains REVERT: A 134 ASP cc_start: 0.7765 (m-30) cc_final: 0.7303 (p0) REVERT: A 291 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6249 (t80) outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 0.1980 time to fit residues: 33.2285 Evaluate side-chains 120 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 52 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7000 Z= 0.182 Angle : 0.695 9.763 9548 Z= 0.310 Chirality : 0.044 0.291 1155 Planarity : 0.005 0.054 1135 Dihedral : 10.884 59.896 1848 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.04 % Allowed : 16.55 % Favored : 80.41 % 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: -0.63 (0.28), residues: 871 helix: 1.60 (0.26), residues: 384 sheet: -0.75 (0.41), residues: 162 loop : -2.84 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 346 HIS 0.003 0.001 HIS A 288 PHE 0.023 0.001 PHE A 367 TYR 0.014 0.001 TYR C 123 ARG 0.004 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.750 Fit side-chains REVERT: A 134 ASP cc_start: 0.7737 (m-30) cc_final: 0.7263 (p0) REVERT: A 325 ASP cc_start: 0.7216 (p0) cc_final: 0.7015 (p0) REVERT: C 190 PHE cc_start: 0.7805 (t80) cc_final: 0.7518 (t80) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.1891 time to fit residues: 30.3820 Evaluate side-chains 122 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 57 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7000 Z= 0.214 Angle : 0.688 9.666 9548 Z= 0.312 Chirality : 0.043 0.283 1155 Planarity : 0.005 0.051 1135 Dihedral : 10.456 59.726 1848 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.38 % Allowed : 17.40 % Favored : 79.22 % 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: -0.59 (0.28), residues: 871 helix: 1.63 (0.26), residues: 385 sheet: -0.75 (0.41), residues: 162 loop : -2.82 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 346 HIS 0.003 0.001 HIS A 288 PHE 0.031 0.002 PHE A 367 TYR 0.016 0.001 TYR C 123 ARG 0.004 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.700 Fit side-chains REVERT: A 291 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6488 (t80) REVERT: C 190 PHE cc_start: 0.7844 (t80) cc_final: 0.7558 (t80) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.1927 time to fit residues: 32.1621 Evaluate side-chains 123 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7000 Z= 0.285 Angle : 0.725 9.969 9548 Z= 0.334 Chirality : 0.044 0.280 1155 Planarity : 0.005 0.052 1135 Dihedral : 10.362 58.549 1848 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.72 % Allowed : 16.89 % Favored : 79.39 % 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: -0.65 (0.28), residues: 871 helix: 1.57 (0.26), residues: 383 sheet: -0.82 (0.41), residues: 162 loop : -2.78 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 346 HIS 0.003 0.001 HIS A 156 PHE 0.029 0.002 PHE A 367 TYR 0.017 0.002 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.924 Fit side-chains REVERT: A 134 ASP cc_start: 0.7718 (m-30) cc_final: 0.7287 (p0) REVERT: A 291 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6332 (t80) REVERT: A 325 ASP cc_start: 0.7442 (p0) cc_final: 0.7182 (p0) REVERT: B 60 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.6806 (mm-40) REVERT: B 168 MET cc_start: 0.7932 (tpt) cc_final: 0.7581 (tpt) REVERT: C 190 PHE cc_start: 0.7845 (t80) cc_final: 0.7337 (t80) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.1951 time to fit residues: 32.4055 Evaluate side-chains 128 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7000 Z= 0.195 Angle : 0.666 9.426 9548 Z= 0.305 Chirality : 0.042 0.276 1155 Planarity : 0.005 0.052 1135 Dihedral : 9.995 59.783 1848 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.55 % Allowed : 17.06 % Favored : 79.39 % 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: -0.50 (0.28), residues: 871 helix: 1.72 (0.26), residues: 381 sheet: -0.73 (0.41), residues: 157 loop : -2.70 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 346 HIS 0.001 0.001 HIS A 156 PHE 0.013 0.001 PHE C 38 TYR 0.019 0.001 TYR C 123 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.669 Fit side-chains REVERT: A 108 ARG cc_start: 0.6362 (ptm-80) cc_final: 0.5924 (ptm160) REVERT: A 291 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6301 (t80) REVERT: B 60 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.6749 (mm-40) REVERT: B 168 MET cc_start: 0.7939 (tpt) cc_final: 0.7536 (tpt) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1902 time to fit residues: 31.1719 Evaluate side-chains 125 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 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 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7000 Z= 0.248 Angle : 0.698 11.589 9548 Z= 0.321 Chirality : 0.043 0.277 1155 Planarity : 0.005 0.052 1135 Dihedral : 9.941 59.898 1848 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.72 % Allowed : 17.91 % Favored : 78.38 % 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: -0.58 (0.28), residues: 871 helix: 1.62 (0.26), residues: 382 sheet: -0.76 (0.41), residues: 157 loop : -2.72 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 346 HIS 0.002 0.001 HIS A 156 PHE 0.018 0.002 PHE A 386 TYR 0.018 0.001 TYR C 123 ARG 0.004 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.687 Fit side-chains REVERT: A 108 ARG cc_start: 0.6522 (ptm-80) cc_final: 0.6054 (ptm160) REVERT: A 291 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6282 (t80) REVERT: A 423 ILE cc_start: 0.8371 (tp) cc_final: 0.8125 (tt) REVERT: B 60 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.6820 (mm-40) REVERT: B 120 LEU cc_start: 0.7629 (tp) cc_final: 0.7426 (tp) REVERT: B 168 MET cc_start: 0.7948 (tpt) cc_final: 0.7537 (tpt) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.1923 time to fit residues: 30.9687 Evaluate side-chains 123 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 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 324 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7000 Z= 0.245 Angle : 0.691 9.927 9548 Z= 0.318 Chirality : 0.043 0.276 1155 Planarity : 0.005 0.051 1135 Dihedral : 9.824 58.047 1848 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.38 % Allowed : 17.91 % Favored : 78.72 % 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: -0.60 (0.28), residues: 871 helix: 1.60 (0.26), residues: 382 sheet: -0.73 (0.41), residues: 157 loop : -2.74 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 346 HIS 0.002 0.001 HIS A 156 PHE 0.016 0.001 PHE C 38 TYR 0.015 0.001 TYR C 123 ARG 0.005 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.767 Fit side-chains REVERT: A 108 ARG cc_start: 0.6528 (ptm-80) cc_final: 0.5983 (ptm160) REVERT: A 291 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6274 (t80) REVERT: A 409 ASP cc_start: 0.8127 (t0) cc_final: 0.7923 (t0) REVERT: B 60 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: B 168 MET cc_start: 0.7957 (tpt) cc_final: 0.7545 (tpt) outliers start: 19 outliers final: 16 residues processed: 122 average time/residue: 0.1946 time to fit residues: 31.7792 Evaluate side-chains 125 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7000 Z= 0.194 Angle : 0.671 9.624 9548 Z= 0.308 Chirality : 0.042 0.276 1155 Planarity : 0.005 0.055 1135 Dihedral : 9.553 58.506 1848 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.21 % Allowed : 18.92 % Favored : 77.87 % 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: -0.52 (0.28), residues: 871 helix: 1.69 (0.27), residues: 381 sheet: -0.70 (0.41), residues: 157 loop : -2.72 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 346 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.001 PHE A 367 TYR 0.022 0.001 TYR C 123 ARG 0.003 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.641 Fit side-chains REVERT: A 108 ARG cc_start: 0.6523 (ptm-80) cc_final: 0.5958 (ptm160) REVERT: A 291 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6280 (t80) REVERT: A 409 ASP cc_start: 0.8154 (t0) cc_final: 0.7927 (t0) REVERT: B 60 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.6766 (mm-40) REVERT: B 168 MET cc_start: 0.7927 (tpt) cc_final: 0.7558 (tpt) REVERT: C 123 TYR cc_start: 0.7971 (m-80) cc_final: 0.7715 (m-10) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 0.1848 time to fit residues: 30.9403 Evaluate side-chains 130 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.168672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142698 restraints weight = 43297.306| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 5.04 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7000 Z= 0.201 Angle : 0.669 9.502 9548 Z= 0.308 Chirality : 0.042 0.276 1155 Planarity : 0.005 0.053 1135 Dihedral : 9.416 58.843 1848 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.87 % Allowed : 18.92 % Favored : 78.21 % 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 (0.28), residues: 871 helix: 1.68 (0.27), residues: 380 sheet: -0.59 (0.42), residues: 151 loop : -2.70 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 346 HIS 0.002 0.001 HIS A 156 PHE 0.026 0.001 PHE A 367 TYR 0.013 0.001 TYR A 251 ARG 0.004 0.001 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.75 seconds wall clock time: 35 minutes 8.23 seconds (2108.23 seconds total)