Starting phenix.real_space_refine on Fri Nov 15 00:36:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/11_2024/8d2v_27151.cif" } resolution = 4.1 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= 0.035 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 1603 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 Na 1 4.78 5 C 4186 2.51 5 N 995 2.21 5 O 1175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 Conformer: "B" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 bond proxies already assigned to first conformer: 3368 Chain: "B" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1375 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1371 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' NA': 1, 'LMT': 8, 'ZGS': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 Time building chain proxies: 7.97, per 1000 atoms: 1.25 Number of scatterers: 6388 At special positions: 0 Unit cell: (71.74, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 1 15.00 Na 1 11.00 O 1175 8.00 N 995 7.00 C 4186 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=2.03 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=2.03 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 45.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 48 through 68 removed outlier: 3.783A pdb=" N GLY A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 100 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.590A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 Processing helix chain 'A' and resid 232 through 262 Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 288 through 320 removed outlier: 3.579A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 351 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.635A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.523A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.522A pdb=" N PHE A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.865A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.005A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.954A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.566A pdb=" N TRP B 143 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58 removed outlier: 5.514A pdb=" N TRP C 46 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE C 38 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.628A pdb=" N VAL C 176 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.628A pdb=" N VAL C 176 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 187 392 hydrogen bonds defined for protein. 1115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 964 1.31 - 1.44: 1856 1.44 - 1.56: 3666 1.56 - 1.69: 36 1.69 - 1.81: 42 Bond restraints: 6564 Sorted by residual: 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 3.84e+01 bond pdb=" C1B LMT A 606 " pdb=" O5B LMT A 606 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C1B LMT A 605 " pdb=" O5B LMT A 605 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1B LMT A 602 " pdb=" O5B LMT A 602 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 8869 5.29 - 10.58: 109 10.58 - 15.87: 5 15.87 - 21.17: 2 21.17 - 26.46: 4 Bond angle restraints: 8989 Sorted by residual: angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 113.18 86.72 26.46 2.37e+00 1.78e-01 1.25e+02 angle pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " ideal model delta sigma weight residual 127.34 152.42 -25.08 3.00e+00 1.11e-01 6.99e+01 angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 152.19 -25.03 3.00e+00 1.11e-01 6.96e+01 angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 152.28 -24.76 3.00e+00 1.11e-01 6.81e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 130.45 -19.75 3.00e+00 1.11e-01 4.33e+01 ... (remaining 8984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 3655 25.37 - 50.74: 199 50.74 - 76.12: 72 76.12 - 101.49: 58 101.49 - 126.86: 74 Dihedral angle restraints: 4058 sinusoidal: 1598 harmonic: 2460 Sorted by residual: dihedral pdb=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O28 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 66.18 -166.96 -126.86 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" O2B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual 63.73 -174.52 -121.75 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual -175.52 -54.27 -121.25 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 4055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 858 0.058 - 0.116: 176 0.116 - 0.175: 29 0.175 - 0.233: 6 0.233 - 0.291: 1 Chirality restraints: 1070 Sorted by residual: 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 -2.49 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C4' LMT A 606 " pdb=" C3' LMT A 606 " pdb=" C5' LMT A 606 " pdb=" O1B LMT A 606 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C1B LMT A 602 " pdb=" C2B LMT A 602 " pdb=" O1B LMT A 602 " pdb=" O5B LMT A 602 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1067 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 103 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO C 104 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO C 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 76 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.031 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1524 2.79 - 3.32: 5616 3.32 - 3.84: 10714 3.84 - 4.37: 11332 4.37 - 4.90: 20286 Nonbonded interactions: 49472 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" OG1 THR A 444 " model vdw 2.262 3.040 nonbonded pdb=" N GLY B 97 " pdb=" O GLY B 97 " model vdw 2.279 2.496 nonbonded pdb=" OD2 ASP A 72 " pdb=" O6B LMT A 606 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 129 " pdb=" O4' LMT A 605 " model vdw 2.308 3.040 nonbonded pdb=" O VAL A 332 " pdb=" OG SER A 336 " model vdw 2.310 3.040 ... (remaining 49467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.010 0.124 6564 Z= 0.621 Angle : 1.275 26.456 8989 Z= 0.535 Chirality : 0.051 0.291 1070 Planarity : 0.007 0.073 1105 Dihedral : 28.636 126.860 2478 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.75 % Allowed : 7.12 % Favored : 92.13 % 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: -1.27 (0.27), residues: 862 helix: 0.05 (0.24), residues: 370 sheet: 0.01 (0.39), residues: 188 loop : -2.51 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 140 HIS 0.001 0.000 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.018 0.002 TYR A 43 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.586 Fit side-chains REVERT: A 242 ILE cc_start: 0.8081 (mt) cc_final: 0.7616 (mm) REVERT: B 70 SER cc_start: 0.8046 (t) cc_final: 0.7226 (m) REVERT: B 72 SER cc_start: 0.8202 (m) cc_final: 0.7856 (p) REVERT: B 154 MET cc_start: 0.8205 (mtt) cc_final: 0.7539 (mtm) REVERT: B 156 TRP cc_start: 0.8406 (m-90) cc_final: 0.7857 (m-90) REVERT: C 81 ILE cc_start: 0.7687 (mm) cc_final: 0.7456 (mt) REVERT: C 136 THR cc_start: 0.9103 (m) cc_final: 0.8872 (p) REVERT: C 190 PHE cc_start: 0.7268 (t80) cc_final: 0.7053 (t80) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.1649 time to fit residues: 41.0382 Evaluate side-chains 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 0.0020 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 135 GLN A 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6564 Z= 0.219 Angle : 0.819 11.662 8989 Z= 0.367 Chirality : 0.055 0.730 1070 Planarity : 0.006 0.057 1105 Dihedral : 16.878 138.854 1430 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.19 % Allowed : 2.06 % Favored : 97.75 % 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: -0.53 (0.28), residues: 862 helix: 1.11 (0.26), residues: 372 sheet: -0.01 (0.41), residues: 176 loop : -2.41 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 140 HIS 0.002 0.001 HIS A 230 PHE 0.031 0.002 PHE A 298 TYR 0.035 0.002 TYR A 358 ARG 0.004 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8260 (tt) cc_final: 0.8022 (tt) REVERT: A 242 ILE cc_start: 0.8080 (mt) cc_final: 0.7634 (mm) REVERT: A 462 GLU cc_start: 0.8096 (mp0) cc_final: 0.7602 (mt-10) REVERT: B 70 SER cc_start: 0.7967 (t) cc_final: 0.7158 (m) REVERT: B 72 SER cc_start: 0.8144 (m) cc_final: 0.7863 (p) REVERT: B 88 LEU cc_start: 0.7538 (pp) cc_final: 0.6404 (mp) REVERT: B 154 MET cc_start: 0.8154 (mtt) cc_final: 0.7651 (mtm) REVERT: B 156 TRP cc_start: 0.8509 (m-90) cc_final: 0.8045 (m-90) REVERT: C 72 GLN cc_start: 0.7957 (pm20) cc_final: 0.7365 (mt0) REVERT: C 81 ILE cc_start: 0.7647 (mm) cc_final: 0.7401 (mm) REVERT: C 112 ASN cc_start: 0.7449 (p0) cc_final: 0.7216 (p0) REVERT: C 137 LEU cc_start: 0.8861 (mt) cc_final: 0.8642 (mt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1462 time to fit residues: 28.5358 Evaluate side-chains 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 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 328 ASN B 134 ASN B 153 ASN C 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 0.044 6564 Z= 0.210 Angle : 0.678 7.116 8989 Z= 0.322 Chirality : 0.045 0.289 1070 Planarity : 0.006 0.058 1105 Dihedral : 12.959 129.981 1430 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % 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: -0.13 (0.29), residues: 862 helix: 1.35 (0.26), residues: 376 sheet: 0.17 (0.40), residues: 195 loop : -2.25 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 135 HIS 0.001 0.000 HIS A 156 PHE 0.026 0.002 PHE A 298 TYR 0.017 0.002 TYR C 123 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ILE cc_start: 0.7956 (mt) cc_final: 0.7564 (mm) REVERT: A 264 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7220 (tp30) REVERT: A 462 GLU cc_start: 0.8163 (mp0) cc_final: 0.7792 (mt-10) REVERT: B 70 SER cc_start: 0.8026 (t) cc_final: 0.7199 (m) REVERT: B 72 SER cc_start: 0.8227 (m) cc_final: 0.7931 (p) REVERT: B 88 LEU cc_start: 0.7582 (pp) cc_final: 0.6438 (mp) REVERT: B 154 MET cc_start: 0.8210 (mtt) cc_final: 0.7955 (mtt) REVERT: B 156 TRP cc_start: 0.8505 (m-90) cc_final: 0.8257 (m-90) REVERT: C 72 GLN cc_start: 0.7975 (pm20) cc_final: 0.6775 (mt0) REVERT: C 81 ILE cc_start: 0.7664 (mm) cc_final: 0.7411 (mm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1671 time to fit residues: 31.0876 Evaluate side-chains 107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 50.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6564 Z= 0.275 Angle : 0.702 6.800 8989 Z= 0.342 Chirality : 0.045 0.258 1070 Planarity : 0.006 0.067 1105 Dihedral : 12.136 121.093 1430 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.19 % Allowed : 1.69 % Favored : 98.13 % 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: -0.20 (0.29), residues: 862 helix: 1.38 (0.27), residues: 377 sheet: -0.08 (0.41), residues: 181 loop : -2.16 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 95 HIS 0.001 0.000 HIS A 230 PHE 0.031 0.002 PHE A 486 TYR 0.020 0.002 TYR A 291 ARG 0.005 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7156 (tp) cc_final: 0.6754 (tt) REVERT: A 421 GLU cc_start: 0.6517 (tt0) cc_final: 0.5999 (tm-30) REVERT: A 462 GLU cc_start: 0.8186 (mp0) cc_final: 0.7851 (mt-10) REVERT: B 70 SER cc_start: 0.8047 (t) cc_final: 0.7176 (m) REVERT: B 72 SER cc_start: 0.8270 (m) cc_final: 0.8008 (p) REVERT: B 88 LEU cc_start: 0.7741 (pp) cc_final: 0.6416 (mp) REVERT: C 72 GLN cc_start: 0.7969 (pm20) cc_final: 0.6715 (mt0) REVERT: C 81 ILE cc_start: 0.7662 (mm) cc_final: 0.7388 (mm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1529 time to fit residues: 27.7444 Evaluate side-chains 106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6564 Z= 0.177 Angle : 0.645 6.739 8989 Z= 0.311 Chirality : 0.043 0.259 1070 Planarity : 0.005 0.056 1105 Dihedral : 11.604 118.125 1430 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % 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: -0.03 (0.29), residues: 862 helix: 1.54 (0.27), residues: 378 sheet: 0.08 (0.41), residues: 178 loop : -2.14 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 PHE 0.031 0.002 PHE A 431 TYR 0.020 0.001 TYR A 291 ARG 0.004 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7914 (tp) cc_final: 0.7690 (tp) REVERT: A 421 GLU cc_start: 0.6284 (tt0) cc_final: 0.5959 (tm-30) REVERT: A 462 GLU cc_start: 0.8133 (mp0) cc_final: 0.7786 (mt-10) REVERT: B 70 SER cc_start: 0.7972 (t) cc_final: 0.7126 (m) REVERT: B 72 SER cc_start: 0.8204 (m) cc_final: 0.7958 (p) REVERT: B 88 LEU cc_start: 0.7398 (pp) cc_final: 0.6482 (mp) REVERT: B 154 MET cc_start: 0.8244 (mtt) cc_final: 0.7840 (mtt) REVERT: C 72 GLN cc_start: 0.7945 (pm20) cc_final: 0.6792 (mt0) REVERT: C 81 ILE cc_start: 0.7629 (mm) cc_final: 0.7385 (mt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1533 time to fit residues: 27.6629 Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6564 Z= 0.214 Angle : 0.652 6.818 8989 Z= 0.316 Chirality : 0.043 0.253 1070 Planarity : 0.005 0.056 1105 Dihedral : 11.386 116.414 1430 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 1.87 % Favored : 97.94 % 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: 0.02 (0.29), residues: 862 helix: 1.61 (0.27), residues: 375 sheet: -0.07 (0.40), residues: 180 loop : -2.01 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 85 HIS 0.000 0.000 HIS A 156 PHE 0.031 0.002 PHE A 431 TYR 0.030 0.002 TYR A 358 ARG 0.005 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7134 (tp) cc_final: 0.6752 (tt) REVERT: A 333 ILE cc_start: 0.8336 (mm) cc_final: 0.8101 (mm) REVERT: A 359 ILE cc_start: 0.9037 (tp) cc_final: 0.8764 (mt) REVERT: A 462 GLU cc_start: 0.8130 (mp0) cc_final: 0.7797 (mt-10) REVERT: B 70 SER cc_start: 0.8000 (t) cc_final: 0.7409 (m) REVERT: B 72 SER cc_start: 0.8253 (m) cc_final: 0.7994 (p) REVERT: B 88 LEU cc_start: 0.7517 (pp) cc_final: 0.6581 (mp) REVERT: B 154 MET cc_start: 0.8273 (mtt) cc_final: 0.7869 (mtt) REVERT: C 72 GLN cc_start: 0.7971 (pm20) cc_final: 0.7144 (mt0) REVERT: C 81 ILE cc_start: 0.7637 (mm) cc_final: 0.7403 (mm) REVERT: C 190 PHE cc_start: 0.7872 (t80) cc_final: 0.7657 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1595 time to fit residues: 28.3554 Evaluate side-chains 107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 chunk 49 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6564 Z= 0.192 Angle : 0.638 6.669 8989 Z= 0.308 Chirality : 0.043 0.251 1070 Planarity : 0.005 0.054 1105 Dihedral : 11.144 115.735 1430 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % 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: 0.05 (0.29), residues: 862 helix: 1.61 (0.27), residues: 377 sheet: 0.00 (0.40), residues: 178 loop : -2.02 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 PHE 0.025 0.002 PHE A 431 TYR 0.017 0.001 TYR A 291 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7319 (mmm) cc_final: 0.6965 (tpt) REVERT: A 189 LEU cc_start: 0.7870 (tp) cc_final: 0.7664 (tp) REVERT: A 328 ASN cc_start: 0.6902 (t0) cc_final: 0.6638 (t0) REVERT: A 359 ILE cc_start: 0.9085 (tp) cc_final: 0.8836 (mt) REVERT: A 462 GLU cc_start: 0.8154 (mp0) cc_final: 0.7824 (mt-10) REVERT: B 70 SER cc_start: 0.8022 (t) cc_final: 0.7248 (m) REVERT: B 72 SER cc_start: 0.8218 (m) cc_final: 0.7971 (p) REVERT: B 88 LEU cc_start: 0.7345 (pp) cc_final: 0.6485 (mp) REVERT: B 120 LEU cc_start: 0.7955 (tt) cc_final: 0.7485 (tp) REVERT: B 154 MET cc_start: 0.8302 (mtt) cc_final: 0.7864 (mtt) REVERT: B 156 TRP cc_start: 0.8897 (m-90) cc_final: 0.8680 (m-90) REVERT: C 72 GLN cc_start: 0.7992 (pm20) cc_final: 0.6758 (mt0) REVERT: C 81 ILE cc_start: 0.7681 (mm) cc_final: 0.7390 (mt) REVERT: C 190 PHE cc_start: 0.7962 (t80) cc_final: 0.7671 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1477 time to fit residues: 26.5356 Evaluate side-chains 108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0030 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 72 optimal weight: 0.0270 chunk 77 optimal weight: 0.4980 overall best weight: 0.4448 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6564 Z= 0.187 Angle : 0.639 6.765 8989 Z= 0.310 Chirality : 0.043 0.247 1070 Planarity : 0.005 0.054 1105 Dihedral : 10.887 115.147 1430 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.69 % 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: 0.05 (0.29), residues: 862 helix: 1.65 (0.27), residues: 379 sheet: -0.12 (0.39), residues: 180 loop : -2.00 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 PHE 0.036 0.002 PHE A 431 TYR 0.034 0.002 TYR A 358 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7129 (tp) cc_final: 0.6769 (tt) REVERT: A 110 MET cc_start: 0.7349 (mmm) cc_final: 0.7016 (tpt) REVERT: A 462 GLU cc_start: 0.8282 (mp0) cc_final: 0.7888 (mt-10) REVERT: B 70 SER cc_start: 0.8099 (t) cc_final: 0.7228 (m) REVERT: B 72 SER cc_start: 0.8226 (m) cc_final: 0.7991 (p) REVERT: B 120 LEU cc_start: 0.7850 (tt) cc_final: 0.7443 (tp) REVERT: B 139 ILE cc_start: 0.7954 (tt) cc_final: 0.6990 (tt) REVERT: B 154 MET cc_start: 0.8286 (mtt) cc_final: 0.7802 (mtt) REVERT: B 156 TRP cc_start: 0.8907 (m-90) cc_final: 0.8636 (m-90) REVERT: C 72 GLN cc_start: 0.8022 (pm20) cc_final: 0.6898 (mt0) REVERT: C 81 ILE cc_start: 0.7624 (mm) cc_final: 0.7354 (mt) REVERT: C 190 PHE cc_start: 0.8049 (t80) cc_final: 0.7741 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1456 time to fit residues: 25.1479 Evaluate side-chains 103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 23 optimal weight: 0.0040 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.2228 ------------------------------------------------------------------------------- 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: 0.7246 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6564 Z= 0.157 Angle : 0.621 9.003 8989 Z= 0.302 Chirality : 0.042 0.245 1070 Planarity : 0.005 0.054 1105 Dihedral : 10.517 112.945 1430 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % 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: 0.11 (0.29), residues: 862 helix: 1.68 (0.26), residues: 380 sheet: 0.01 (0.40), residues: 178 loop : -2.02 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.034 0.001 PHE A 431 TYR 0.019 0.001 TYR A 291 ARG 0.006 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7244 (mmm) cc_final: 0.6950 (tpt) REVERT: A 315 PHE cc_start: 0.8096 (t80) cc_final: 0.7601 (t80) REVERT: A 462 GLU cc_start: 0.8233 (mp0) cc_final: 0.7881 (mt-10) REVERT: B 70 SER cc_start: 0.8003 (t) cc_final: 0.7170 (m) REVERT: B 72 SER cc_start: 0.8156 (m) cc_final: 0.7919 (p) REVERT: B 120 LEU cc_start: 0.7871 (tt) cc_final: 0.7446 (tp) REVERT: B 154 MET cc_start: 0.8289 (mtt) cc_final: 0.7853 (mtt) REVERT: C 72 GLN cc_start: 0.7984 (pm20) cc_final: 0.6937 (mt0) REVERT: C 81 ILE cc_start: 0.7680 (mm) cc_final: 0.7387 (mt) REVERT: C 190 PHE cc_start: 0.8076 (t80) cc_final: 0.7633 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1591 time to fit residues: 26.5367 Evaluate side-chains 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6564 Z= 0.177 Angle : 0.636 8.575 8989 Z= 0.305 Chirality : 0.042 0.241 1070 Planarity : 0.005 0.054 1105 Dihedral : 10.369 111.618 1430 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % 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: 0.14 (0.29), residues: 862 helix: 1.69 (0.26), residues: 380 sheet: -0.03 (0.40), residues: 180 loop : -1.96 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 46 HIS 0.001 0.000 HIS A 156 PHE 0.034 0.001 PHE A 431 TYR 0.024 0.002 TYR A 358 ARG 0.008 0.001 ARG C 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7301 (mmm) cc_final: 0.7052 (tpt) REVERT: A 112 TRP cc_start: 0.6968 (m100) cc_final: 0.6645 (m-10) REVERT: A 315 PHE cc_start: 0.8074 (t80) cc_final: 0.7649 (t80) REVERT: A 462 GLU cc_start: 0.8240 (mp0) cc_final: 0.7896 (mt-10) REVERT: B 70 SER cc_start: 0.8047 (t) cc_final: 0.7186 (m) REVERT: B 72 SER cc_start: 0.8183 (m) cc_final: 0.7958 (p) REVERT: B 154 MET cc_start: 0.8151 (mtt) cc_final: 0.7885 (mtt) REVERT: B 156 TRP cc_start: 0.8857 (m-90) cc_final: 0.8639 (m-90) REVERT: C 72 GLN cc_start: 0.7989 (pm20) cc_final: 0.6892 (mt0) REVERT: C 81 ILE cc_start: 0.7608 (mm) cc_final: 0.7362 (mt) REVERT: C 190 PHE cc_start: 0.8075 (t80) cc_final: 0.7698 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1531 time to fit residues: 25.9609 Evaluate side-chains 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 70 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152706 restraints weight = 29691.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150577 restraints weight = 29948.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147158 restraints weight = 14058.399| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6564 Z= 0.153 Angle : 0.619 8.257 8989 Z= 0.299 Chirality : 0.041 0.240 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.061 114.972 1430 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.63 % 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: 0.22 (0.29), residues: 862 helix: 1.72 (0.26), residues: 380 sheet: 0.16 (0.41), residues: 178 loop : -1.97 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.032 0.001 PHE A 431 TYR 0.019 0.001 TYR A 291 ARG 0.006 0.001 ARG C 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.46 seconds wall clock time: 33 minutes 11.75 seconds (1991.75 seconds total)