Starting phenix.real_space_refine on Thu Jul 2 06:08:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3k_66502/07_2026/9x3k_66502.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4377 2.51 5 N 1149 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6885 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2170 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 5 Chain: "B" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2170 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 5 Chain: "C" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2170 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 5 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.18 Number of scatterers: 6885 At special positions: 0 Unit cell: (89.59, 94.792, 74.562, 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 1326 8.00 N 1149 7.00 C 4377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 492 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 492 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 492 " - pdb=" SG CYS C 537 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 701 " - " ASN A 179 " " NAG B 701 " - " ASN B 179 " " NAG C 701 " - " ASN C 179 " " NAG D 1 " - " ASN A 544 " " NAG E 1 " - " ASN A 102 " " NAG F 1 " - " ASN B 544 " " NAG G 1 " - " ASN B 102 " " NAG H 1 " - " ASN C 544 " " NAG I 1 " - " ASN C 102 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 23.1% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 534 through 557 removed outlier: 4.732A pdb=" N LYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'B' and resid 519 through 522 Processing helix chain 'B' and resid 533 through 557 removed outlier: 4.138A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B 549 " --> pdb=" O GLN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 179 through 187 Processing helix chain 'C' and resid 519 through 522 Processing helix chain 'C' and resid 534 through 557 removed outlier: 4.687A pdb=" N LYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C 549 " --> pdb=" O GLN C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 569 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 470 through 474 removed outlier: 7.051A pdb=" N VAL A 30 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU A 93 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU A 57 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU A 95 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER A 59 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 474 removed outlier: 7.051A pdb=" N VAL A 30 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR A 88 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 106 Processing sheet with id=AA5, first strand: chain 'B' and resid 470 through 474 removed outlier: 3.779A pdb=" N VAL B 30 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU B 93 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU B 57 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU B 95 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER B 59 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 470 through 474 removed outlier: 3.779A pdb=" N VAL B 30 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B 88 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 81 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 106 removed outlier: 6.581A pdb=" N ILE B 130 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TRP B 206 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS B 132 " --> pdb=" O TRP B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 470 through 474 removed outlier: 3.575A pdb=" N VAL C 30 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU C 93 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU C 57 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU C 95 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER C 59 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 470 through 474 removed outlier: 3.575A pdb=" N VAL C 30 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C 88 " --> pdb=" O TYR C 563 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 106 231 hydrogen bonds defined for protein. 639 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: 1.01 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2120 1.34 - 1.46: 1675 1.46 - 1.58: 3174 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 7020 Sorted by residual: bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.458 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" C1 MAN H 5 " pdb=" C2 MAN H 5 " ideal model delta sigma weight residual 1.526 1.576 -0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" C5 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" CA ASP C 491 " pdb=" CB ASP C 491 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.21e-02 6.83e+03 4.81e+00 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 9359 3.47 - 6.93: 125 6.93 - 10.40: 10 10.40 - 13.86: 0 13.86 - 17.33: 1 Bond angle restraints: 9495 Sorted by residual: angle pdb=" CA LEU C 218 " pdb=" CB LEU C 218 " pdb=" CG LEU C 218 " ideal model delta sigma weight residual 116.30 133.63 -17.33 3.50e+00 8.16e-02 2.45e+01 angle pdb=" CA LYS A 188 " pdb=" CB LYS A 188 " pdb=" CG LYS A 188 " ideal model delta sigma weight residual 114.10 123.29 -9.19 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA LYS B 188 " pdb=" CB LYS B 188 " pdb=" CG LYS B 188 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C LYS A 188 " pdb=" N ILE A 189 " pdb=" CA ILE A 189 " ideal model delta sigma weight residual 121.97 129.67 -7.70 1.80e+00 3.09e-01 1.83e+01 angle pdb=" CA LYS C 188 " pdb=" CB LYS C 188 " pdb=" CG LYS C 188 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.78e+01 ... (remaining 9490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 4209 21.97 - 43.94: 276 43.94 - 65.91: 22 65.91 - 87.88: 46 87.88 - 109.84: 25 Dihedral angle restraints: 4578 sinusoidal: 2202 harmonic: 2376 Sorted by residual: dihedral pdb=" CA LYS C 188 " pdb=" C LYS C 188 " pdb=" N ILE C 189 " pdb=" CA ILE C 189 " ideal model delta harmonic sigma weight residual 180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN C 179 " pdb=" C ASN C 179 " pdb=" N LYS C 180 " pdb=" CA LYS C 180 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LYS B 188 " pdb=" C LYS B 188 " pdb=" N ILE B 189 " pdb=" CA ILE B 189 " ideal model delta harmonic sigma weight residual 180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 951 0.062 - 0.123: 170 0.123 - 0.185: 42 0.185 - 0.246: 7 0.246 - 0.308: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1173 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 78 " -0.023 2.00e-02 2.50e+03 2.55e-02 1.62e+01 pdb=" CG TRP A 78 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 78 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 78 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 78 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 78 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 78 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 78 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 188 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C LYS C 188 " 0.062 2.00e-02 2.50e+03 pdb=" O LYS C 188 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE C 189 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 188 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS A 188 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS A 188 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 189 " -0.021 2.00e-02 2.50e+03 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1198 2.78 - 3.31: 5622 3.31 - 3.84: 10787 3.84 - 4.37: 12736 4.37 - 4.90: 22990 Nonbonded interactions: 53333 Sorted by model distance: nonbonded pdb=" O LEU C 542 " pdb=" OG1 THR C 546 " model vdw 2.250 3.040 nonbonded pdb=" O LEU B 542 " pdb=" OG1 THR B 546 " model vdw 2.256 3.040 nonbonded pdb=" O LEU A 542 " pdb=" OG1 THR A 546 " model vdw 2.263 3.040 nonbonded pdb=" OG SER C 75 " pdb=" O VAL C 220 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A 75 " pdb=" O VAL A 220 " model vdw 2.305 3.040 ... (remaining 53328 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.006 0.059 7056 Z= 0.274 Angle : 0.995 17.326 9597 Z= 0.479 Chirality : 0.058 0.308 1176 Planarity : 0.007 0.053 1140 Dihedral : 18.210 109.844 3012 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.27), residues: 786 helix: -1.92 (0.31), residues: 186 sheet: -0.78 (0.33), residues: 255 loop : -1.72 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 207 TYR 0.021 0.002 TYR A 474 PHE 0.018 0.003 PHE A 168 TRP 0.065 0.003 TRP A 78 HIS 0.006 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 ( 7020) covalent geometry : angle 0.96913 / 0.47 ( 9495) SS BOND : bond 0.00037 / 0.03 ( 6) SS BOND : angle 0.66995 / 0.44 ( 12) hydrogen bonds : bond 0.15052 / 9.64 ( 215) hydrogen bonds : angle 5.85282 / 3.98 ( 639) link_ALPHA1-3 : bond 0.00608 / 0.50 ( 6) link_ALPHA1-3 : angle 1.77250 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00317 / 0.18 ( 3) link_ALPHA1-6 : angle 1.58461 / 0.98 ( 9) link_BETA1-4 : bond 0.00606 / 0.39 ( 12) link_BETA1-4 : angle 2.96045 / 1.80 ( 36) link_NAG-ASN : bond 0.00499 / 0.37 ( 9) link_NAG-ASN : angle 2.60711 / 1.69 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.183 Fit side-chains REVERT: A 34 ILE cc_start: 0.8486 (mt) cc_final: 0.8282 (mm) REVERT: A 109 GLN cc_start: 0.8025 (mp10) cc_final: 0.7654 (mp10) REVERT: A 119 SER cc_start: 0.8475 (m) cc_final: 0.8264 (p) REVERT: A 128 LYS cc_start: 0.8492 (mttp) cc_final: 0.8254 (mttp) REVERT: A 191 LYS cc_start: 0.7743 (mppt) cc_final: 0.7515 (mmtm) REVERT: A 538 ARG cc_start: 0.7629 (mtp180) cc_final: 0.6948 (mtp180) REVERT: B 34 ILE cc_start: 0.8280 (mt) cc_final: 0.8050 (mm) REVERT: B 49 VAL cc_start: 0.8651 (t) cc_final: 0.8401 (p) REVERT: B 66 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8605 (mtpt) REVERT: B 109 GLN cc_start: 0.8070 (mp10) cc_final: 0.7847 (mp10) REVERT: B 128 LYS cc_start: 0.8445 (mttp) cc_final: 0.7903 (mttp) REVERT: B 164 LYS cc_start: 0.9284 (tttp) cc_final: 0.8973 (tttp) REVERT: C 51 LYS cc_start: 0.8585 (mttm) cc_final: 0.8267 (mtmm) REVERT: C 109 GLN cc_start: 0.8290 (mp10) cc_final: 0.8071 (mp10) REVERT: C 128 LYS cc_start: 0.8379 (mttp) cc_final: 0.8028 (mttp) REVERT: C 472 MET cc_start: 0.7525 (ttt) cc_final: 0.7226 (ttm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1190 time to fit residues: 31.9670 Evaluate side-chains 185 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN B 545 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089126 restraints weight = 11481.543| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.61 r_work: 0.3055 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7056 Z= 0.161 Angle : 0.665 5.773 9597 Z= 0.318 Chirality : 0.045 0.264 1176 Planarity : 0.004 0.036 1140 Dihedral : 12.446 72.405 1467 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.28 % Allowed : 8.09 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.28), residues: 786 helix: -0.80 (0.37), residues: 168 sheet: -0.34 (0.33), residues: 249 loop : -1.15 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 207 TYR 0.008 0.001 TYR C 563 PHE 0.013 0.002 PHE C 91 TRP 0.020 0.001 TRP A 78 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7020) covalent geometry : angle 0.62835 / 0.31 ( 9495) SS BOND : bond 0.00046 / 0.03 ( 6) SS BOND : angle 0.51454 / 0.32 ( 12) hydrogen bonds : bond 0.04586 / 2.92 ( 215) hydrogen bonds : angle 4.40982 / 3.00 ( 639) link_ALPHA1-3 : bond 0.00681 / 0.53 ( 6) link_ALPHA1-3 : angle 2.05032 / 1.26 ( 18) link_ALPHA1-6 : bond 0.00401 / 0.23 ( 3) link_ALPHA1-6 : angle 1.96333 / 1.17 ( 9) link_BETA1-4 : bond 0.00302 / 0.20 ( 12) link_BETA1-4 : angle 2.71449 / 1.81 ( 36) link_NAG-ASN : bond 0.00315 / 0.23 ( 9) link_NAG-ASN : angle 2.11616 / 1.31 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7883 (m-30) cc_final: 0.7624 (m-30) REVERT: A 119 SER cc_start: 0.8881 (m) cc_final: 0.8582 (p) REVERT: B 49 VAL cc_start: 0.8735 (t) cc_final: 0.8506 (p) REVERT: B 76 LYS cc_start: 0.9125 (mttt) cc_final: 0.8886 (mtmm) REVERT: B 136 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 553 LEU cc_start: 0.8143 (mt) cc_final: 0.7863 (mp) REVERT: C 49 VAL cc_start: 0.8758 (t) cc_final: 0.8508 (p) REVERT: C 51 LYS cc_start: 0.8873 (mttm) cc_final: 0.8359 (mtmm) REVERT: C 111 ARG cc_start: 0.7822 (ptp90) cc_final: 0.7585 (ptp-170) REVERT: C 128 LYS cc_start: 0.8422 (mttp) cc_final: 0.8183 (mttp) REVERT: C 472 MET cc_start: 0.8107 (ttt) cc_final: 0.7708 (ttt) REVERT: C 538 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7546 (mtp-110) outliers start: 9 outliers final: 5 residues processed: 195 average time/residue: 0.1192 time to fit residues: 27.9757 Evaluate side-chains 197 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN B 545 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087884 restraints weight = 11457.078| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.60 r_work: 0.3029 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7056 Z= 0.160 Angle : 0.645 7.184 9597 Z= 0.307 Chirality : 0.045 0.228 1176 Planarity : 0.004 0.031 1140 Dihedral : 9.265 59.143 1467 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.55 % Allowed : 10.64 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.28), residues: 786 helix: -0.42 (0.38), residues: 168 sheet: -0.15 (0.33), residues: 249 loop : -1.06 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 207 TYR 0.011 0.001 TYR C 563 PHE 0.016 0.002 PHE C 26 TRP 0.014 0.001 TRP A 78 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7020) covalent geometry : angle 0.61534 / 0.30 ( 9495) SS BOND : bond 0.00064 / 0.05 ( 6) SS BOND : angle 0.51928 / 0.30 ( 12) hydrogen bonds : bond 0.04495 / 2.89 ( 215) hydrogen bonds : angle 4.25779 / 2.88 ( 639) link_ALPHA1-3 : bond 0.00731 / 0.53 ( 6) link_ALPHA1-3 : angle 1.66372 / 1.01 ( 18) link_ALPHA1-6 : bond 0.00341 / 0.20 ( 3) link_ALPHA1-6 : angle 1.71839 / 1.11 ( 9) link_BETA1-4 : bond 0.00472 / 0.32 ( 12) link_BETA1-4 : angle 2.43272 / 1.60 ( 36) link_NAG-ASN : bond 0.00320 / 0.23 ( 9) link_NAG-ASN : angle 1.91991 / 1.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7914 (m-30) cc_final: 0.7663 (m-30) REVERT: A 58 MET cc_start: 0.8730 (mtp) cc_final: 0.8479 (mtp) REVERT: A 107 ASP cc_start: 0.8089 (p0) cc_final: 0.7853 (p0) REVERT: A 109 GLN cc_start: 0.8218 (mp10) cc_final: 0.7959 (mp10) REVERT: A 119 SER cc_start: 0.8898 (m) cc_final: 0.8656 (p) REVERT: B 49 VAL cc_start: 0.8738 (t) cc_final: 0.8509 (p) REVERT: B 54 ASP cc_start: 0.8012 (m-30) cc_final: 0.7792 (m-30) REVERT: B 66 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8394 (mtmt) REVERT: B 164 LYS cc_start: 0.9178 (tttp) cc_final: 0.8882 (tttp) REVERT: B 469 ARG cc_start: 0.7253 (mmm-85) cc_final: 0.6905 (ttp80) REVERT: B 472 MET cc_start: 0.7971 (ttt) cc_final: 0.7756 (ttp) REVERT: C 49 VAL cc_start: 0.8794 (t) cc_final: 0.8536 (p) REVERT: C 51 LYS cc_start: 0.8842 (mttm) cc_final: 0.8408 (mtmm) REVERT: C 574 LEU cc_start: 0.9196 (tt) cc_final: 0.8977 (tp) outliers start: 18 outliers final: 12 residues processed: 198 average time/residue: 0.1111 time to fit residues: 26.6237 Evaluate side-chains 193 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087387 restraints weight = 11373.984| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.57 r_work: 0.3032 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7056 Z= 0.183 Angle : 0.643 7.409 9597 Z= 0.307 Chirality : 0.045 0.267 1176 Planarity : 0.004 0.032 1140 Dihedral : 7.654 46.437 1467 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.41 % Allowed : 13.33 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 786 helix: -0.33 (0.38), residues: 168 sheet: -0.11 (0.33), residues: 243 loop : -0.97 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 207 TYR 0.009 0.001 TYR C 563 PHE 0.016 0.002 PHE A 26 TRP 0.008 0.001 TRP A 206 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 7020) covalent geometry : angle 0.61318 / 0.30 ( 9495) SS BOND : bond 0.00071 / 0.05 ( 6) SS BOND : angle 0.47851 / 0.28 ( 12) hydrogen bonds : bond 0.04397 / 2.83 ( 215) hydrogen bonds : angle 4.25353 / 2.88 ( 639) link_ALPHA1-3 : bond 0.00762 / 0.56 ( 6) link_ALPHA1-3 : angle 1.74291 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00225 / 0.13 ( 3) link_ALPHA1-6 : angle 1.98214 / 1.24 ( 9) link_BETA1-4 : bond 0.00359 / 0.22 ( 12) link_BETA1-4 : angle 2.28048 / 1.49 ( 36) link_NAG-ASN : bond 0.00340 / 0.24 ( 9) link_NAG-ASN : angle 2.13992 / 1.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8134 (m-30) cc_final: 0.7896 (m-30) REVERT: A 58 MET cc_start: 0.8803 (mtp) cc_final: 0.8570 (mtp) REVERT: A 111 ARG cc_start: 0.7870 (ptp90) cc_final: 0.7648 (ptp90) REVERT: A 119 SER cc_start: 0.8940 (m) cc_final: 0.8734 (p) REVERT: B 49 VAL cc_start: 0.8829 (t) cc_final: 0.8571 (p) REVERT: B 54 ASP cc_start: 0.8182 (m-30) cc_final: 0.7905 (m-30) REVERT: B 66 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8422 (mtmt) REVERT: B 164 LYS cc_start: 0.9218 (tttp) cc_final: 0.8970 (tttp) REVERT: B 469 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7207 (ttp-170) REVERT: C 49 VAL cc_start: 0.8877 (t) cc_final: 0.8610 (p) REVERT: C 51 LYS cc_start: 0.8924 (mttm) cc_final: 0.8561 (mtmm) REVERT: C 119 SER cc_start: 0.9026 (t) cc_final: 0.8687 (p) outliers start: 17 outliers final: 13 residues processed: 198 average time/residue: 0.1204 time to fit residues: 29.0761 Evaluate side-chains 204 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 561 ARG Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.0040 chunk 67 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088276 restraints weight = 11274.924| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.52 r_work: 0.3055 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7056 Z= 0.126 Angle : 0.605 7.940 9597 Z= 0.291 Chirality : 0.044 0.312 1176 Planarity : 0.004 0.031 1140 Dihedral : 6.782 37.910 1467 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.12 % Allowed : 14.61 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.28), residues: 786 helix: -0.10 (0.38), residues: 171 sheet: -0.03 (0.33), residues: 243 loop : -0.93 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 207 TYR 0.007 0.001 TYR C 563 PHE 0.018 0.002 PHE A 26 TRP 0.007 0.001 TRP A 206 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7020) covalent geometry : angle 0.57713 / 0.29 ( 9495) SS BOND : bond 0.00060 / 0.04 ( 6) SS BOND : angle 0.48769 / 0.28 ( 12) hydrogen bonds : bond 0.03931 / 2.55 ( 215) hydrogen bonds : angle 4.23852 / 2.86 ( 639) link_ALPHA1-3 : bond 0.00870 / 0.61 ( 6) link_ALPHA1-3 : angle 1.55726 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00315 / 0.18 ( 3) link_ALPHA1-6 : angle 1.78945 / 1.15 ( 9) link_BETA1-4 : bond 0.00392 / 0.26 ( 12) link_BETA1-4 : angle 1.98495 / 1.30 ( 36) link_NAG-ASN : bond 0.00486 / 0.35 ( 9) link_NAG-ASN : angle 2.24557 / 1.31 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8121 (m-30) cc_final: 0.7862 (m-30) REVERT: A 111 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7564 (ptp90) REVERT: A 119 SER cc_start: 0.8933 (m) cc_final: 0.8732 (p) REVERT: B 49 VAL cc_start: 0.8813 (t) cc_final: 0.8557 (p) REVERT: B 54 ASP cc_start: 0.8154 (m-30) cc_final: 0.7863 (m-30) REVERT: B 66 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8421 (mtmt) REVERT: B 95 GLU cc_start: 0.8289 (tt0) cc_final: 0.8015 (tt0) REVERT: B 469 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7188 (ttp-170) REVERT: C 49 VAL cc_start: 0.8859 (t) cc_final: 0.8585 (p) REVERT: C 51 LYS cc_start: 0.8904 (mttm) cc_final: 0.8522 (mtmm) REVERT: C 119 SER cc_start: 0.9008 (t) cc_final: 0.8684 (p) REVERT: C 469 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7510 (ttm170) outliers start: 22 outliers final: 16 residues processed: 195 average time/residue: 0.1276 time to fit residues: 30.2816 Evaluate side-chains 204 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086337 restraints weight = 11326.867| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.56 r_work: 0.3017 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7056 Z= 0.209 Angle : 0.654 8.399 9597 Z= 0.314 Chirality : 0.046 0.258 1176 Planarity : 0.004 0.031 1140 Dihedral : 6.377 31.329 1467 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.55 % Allowed : 14.33 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.28), residues: 786 helix: -0.23 (0.38), residues: 174 sheet: -0.06 (0.33), residues: 243 loop : -0.94 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 207 TYR 0.010 0.001 TYR C 563 PHE 0.017 0.002 PHE C 26 TRP 0.009 0.001 TRP A 206 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 7020) covalent geometry : angle 0.62599 / 0.31 ( 9495) SS BOND : bond 0.00082 / 0.06 ( 6) SS BOND : angle 0.37211 / 0.23 ( 12) hydrogen bonds : bond 0.04530 / 2.94 ( 215) hydrogen bonds : angle 4.29216 / 2.91 ( 639) link_ALPHA1-3 : bond 0.00773 / 0.55 ( 6) link_ALPHA1-3 : angle 1.78982 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00266 / 0.15 ( 3) link_ALPHA1-6 : angle 1.86570 / 1.21 ( 9) link_BETA1-4 : bond 0.00369 / 0.23 ( 12) link_BETA1-4 : angle 1.99374 / 1.29 ( 36) link_NAG-ASN : bond 0.00609 / 0.42 ( 9) link_NAG-ASN : angle 2.32171 / 1.37 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8119 (m-30) cc_final: 0.7876 (m-30) REVERT: A 111 ARG cc_start: 0.7917 (ptp90) cc_final: 0.7568 (ptp90) REVERT: B 49 VAL cc_start: 0.8863 (t) cc_final: 0.8596 (p) REVERT: B 54 ASP cc_start: 0.8134 (m-30) cc_final: 0.7845 (m-30) REVERT: B 66 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8439 (mtmt) REVERT: B 119 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 469 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7311 (ttp-170) REVERT: C 49 VAL cc_start: 0.8903 (t) cc_final: 0.8635 (p) REVERT: C 51 LYS cc_start: 0.8941 (mttm) cc_final: 0.8575 (mtmm) REVERT: C 119 SER cc_start: 0.9036 (t) cc_final: 0.8731 (p) outliers start: 25 outliers final: 16 residues processed: 193 average time/residue: 0.1136 time to fit residues: 26.6278 Evaluate side-chains 198 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 545 GLN B 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086662 restraints weight = 11238.861| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.55 r_work: 0.3021 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7056 Z= 0.181 Angle : 0.638 8.239 9597 Z= 0.309 Chirality : 0.045 0.289 1176 Planarity : 0.004 0.031 1140 Dihedral : 5.942 26.863 1467 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.84 % Allowed : 16.17 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.28), residues: 786 helix: -0.14 (0.38), residues: 171 sheet: -0.10 (0.33), residues: 243 loop : -0.95 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 207 TYR 0.009 0.001 TYR C 563 PHE 0.016 0.002 PHE A 26 TRP 0.010 0.001 TRP A 206 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 7020) covalent geometry : angle 0.61159 / 0.30 ( 9495) SS BOND : bond 0.00046 / 0.03 ( 6) SS BOND : angle 0.32924 / 0.20 ( 12) hydrogen bonds : bond 0.04317 / 2.81 ( 215) hydrogen bonds : angle 4.35264 / 2.96 ( 639) link_ALPHA1-3 : bond 0.00783 / 0.57 ( 6) link_ALPHA1-3 : angle 1.62554 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00366 / 0.20 ( 3) link_ALPHA1-6 : angle 1.72891 / 1.14 ( 9) link_BETA1-4 : bond 0.00360 / 0.23 ( 12) link_BETA1-4 : angle 1.95977 / 1.26 ( 36) link_NAG-ASN : bond 0.00409 / 0.28 ( 9) link_NAG-ASN : angle 2.27457 / 1.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8094 (m-30) cc_final: 0.7843 (m-30) REVERT: A 111 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7501 (ptp90) REVERT: B 49 VAL cc_start: 0.8871 (t) cc_final: 0.8598 (p) REVERT: B 54 ASP cc_start: 0.8090 (m-30) cc_final: 0.7818 (m-30) REVERT: B 66 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8437 (mtmt) REVERT: B 93 GLU cc_start: 0.8829 (pt0) cc_final: 0.8593 (pt0) REVERT: B 95 GLU cc_start: 0.8274 (tt0) cc_final: 0.7963 (tt0) REVERT: B 119 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 469 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7339 (ttp-170) REVERT: B 553 LEU cc_start: 0.8229 (mt) cc_final: 0.7973 (mp) REVERT: B 572 ASP cc_start: 0.8209 (m-30) cc_final: 0.7857 (m-30) REVERT: C 49 VAL cc_start: 0.8903 (t) cc_final: 0.8624 (p) REVERT: C 51 LYS cc_start: 0.8911 (mttm) cc_final: 0.8544 (mtmm) REVERT: C 119 SER cc_start: 0.9000 (t) cc_final: 0.8700 (p) outliers start: 20 outliers final: 15 residues processed: 194 average time/residue: 0.1184 time to fit residues: 27.8706 Evaluate side-chains 200 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088023 restraints weight = 11340.471| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.59 r_work: 0.3046 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7056 Z= 0.126 Angle : 0.609 8.438 9597 Z= 0.297 Chirality : 0.044 0.319 1176 Planarity : 0.003 0.034 1140 Dihedral : 5.514 25.007 1467 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 16.17 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.29), residues: 786 helix: 0.07 (0.37), residues: 189 sheet: -0.02 (0.33), residues: 243 loop : -1.01 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 207 TYR 0.006 0.001 TYR C 563 PHE 0.018 0.001 PHE A 26 TRP 0.008 0.001 TRP A 206 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7020) covalent geometry : angle 0.58255 / 0.29 ( 9495) SS BOND : bond 0.00059 / 0.04 ( 6) SS BOND : angle 0.46703 / 0.28 ( 12) hydrogen bonds : bond 0.03860 / 2.50 ( 215) hydrogen bonds : angle 4.30399 / 2.92 ( 639) link_ALPHA1-3 : bond 0.00867 / 0.60 ( 6) link_ALPHA1-3 : angle 1.51670 / 0.92 ( 18) link_ALPHA1-6 : bond 0.00451 / 0.25 ( 3) link_ALPHA1-6 : angle 1.57694 / 1.06 ( 9) link_BETA1-4 : bond 0.00384 / 0.25 ( 12) link_BETA1-4 : angle 1.80890 / 1.17 ( 36) link_NAG-ASN : bond 0.00546 / 0.37 ( 9) link_NAG-ASN : angle 2.39985 / 1.42 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8086 (m-30) cc_final: 0.7831 (m-30) REVERT: B 49 VAL cc_start: 0.8860 (t) cc_final: 0.8598 (p) REVERT: B 54 ASP cc_start: 0.8081 (m-30) cc_final: 0.7811 (m-30) REVERT: B 66 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8410 (mtmt) REVERT: B 93 GLU cc_start: 0.8844 (pt0) cc_final: 0.8601 (pt0) REVERT: B 191 LYS cc_start: 0.8055 (mppt) cc_final: 0.7813 (mmtm) REVERT: B 469 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7340 (ttp-170) REVERT: B 553 LEU cc_start: 0.8192 (mt) cc_final: 0.7932 (mp) REVERT: B 572 ASP cc_start: 0.8157 (m-30) cc_final: 0.7811 (m-30) REVERT: C 49 VAL cc_start: 0.8874 (t) cc_final: 0.8623 (p) REVERT: C 51 LYS cc_start: 0.8884 (mttm) cc_final: 0.8539 (mtmm) REVERT: C 54 ASP cc_start: 0.8256 (m-30) cc_final: 0.7996 (t0) REVERT: C 119 SER cc_start: 0.9017 (t) cc_final: 0.8711 (p) outliers start: 18 outliers final: 14 residues processed: 187 average time/residue: 0.1119 time to fit residues: 25.6828 Evaluate side-chains 195 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086204 restraints weight = 11329.499| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.57 r_work: 0.3002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7056 Z= 0.243 Angle : 0.681 9.775 9597 Z= 0.329 Chirality : 0.047 0.311 1176 Planarity : 0.004 0.034 1140 Dihedral : 5.737 25.202 1467 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 786 helix: -0.17 (0.37), residues: 189 sheet: -0.12 (0.33), residues: 243 loop : -1.08 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 207 TYR 0.011 0.001 TYR C 563 PHE 0.021 0.002 PHE A 26 TRP 0.009 0.001 TRP A 206 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 ( 7020) covalent geometry : angle 0.65259 / 0.32 ( 9495) SS BOND : bond 0.00077 / 0.05 ( 6) SS BOND : angle 0.37614 / 0.22 ( 12) hydrogen bonds : bond 0.04741 / 3.09 ( 215) hydrogen bonds : angle 4.37400 / 2.97 ( 639) link_ALPHA1-3 : bond 0.00683 / 0.48 ( 6) link_ALPHA1-3 : angle 1.82191 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00327 / 0.18 ( 3) link_ALPHA1-6 : angle 1.75331 / 1.17 ( 9) link_BETA1-4 : bond 0.00396 / 0.26 ( 12) link_BETA1-4 : angle 1.88555 / 1.21 ( 36) link_NAG-ASN : bond 0.00422 / 0.29 ( 9) link_NAG-ASN : angle 2.62451 / 1.55 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8106 (m-30) cc_final: 0.7858 (m-30) REVERT: A 111 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7552 (ptp90) REVERT: B 49 VAL cc_start: 0.8902 (t) cc_final: 0.8625 (p) REVERT: B 54 ASP cc_start: 0.8101 (m-30) cc_final: 0.7818 (m-30) REVERT: B 95 GLU cc_start: 0.8406 (tt0) cc_final: 0.8131 (tt0) REVERT: B 191 LYS cc_start: 0.8013 (mppt) cc_final: 0.7719 (mmtm) REVERT: B 553 LEU cc_start: 0.8253 (mt) cc_final: 0.8004 (mp) REVERT: B 572 ASP cc_start: 0.8173 (m-30) cc_final: 0.7864 (m-30) REVERT: C 49 VAL cc_start: 0.8904 (t) cc_final: 0.8621 (p) REVERT: C 51 LYS cc_start: 0.8914 (mttm) cc_final: 0.8507 (mtmm) REVERT: C 54 ASP cc_start: 0.8257 (m-30) cc_final: 0.7987 (t0) REVERT: C 119 SER cc_start: 0.9013 (t) cc_final: 0.8729 (p) REVERT: C 538 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7940 (mtp-110) outliers start: 16 outliers final: 13 residues processed: 194 average time/residue: 0.1228 time to fit residues: 28.8200 Evaluate side-chains 197 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN B 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086791 restraints weight = 11242.999| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.57 r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7056 Z= 0.162 Angle : 0.642 9.168 9597 Z= 0.314 Chirality : 0.045 0.371 1176 Planarity : 0.003 0.035 1140 Dihedral : 5.515 25.670 1467 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 17.16 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 786 helix: -0.10 (0.37), residues: 189 sheet: -0.03 (0.33), residues: 243 loop : -1.03 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 207 TYR 0.007 0.001 TYR C 563 PHE 0.018 0.002 PHE A 26 TRP 0.010 0.001 TRP A 206 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 7020) covalent geometry : angle 0.61513 / 0.31 ( 9495) SS BOND : bond 0.00121 / 0.07 ( 6) SS BOND : angle 0.45630 / 0.26 ( 12) hydrogen bonds : bond 0.04205 / 2.74 ( 215) hydrogen bonds : angle 4.40593 / 2.99 ( 639) link_ALPHA1-3 : bond 0.00779 / 0.54 ( 6) link_ALPHA1-3 : angle 1.56037 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00407 / 0.23 ( 3) link_ALPHA1-6 : angle 1.62510 / 1.10 ( 9) link_BETA1-4 : bond 0.00386 / 0.25 ( 12) link_BETA1-4 : angle 1.78422 / 1.14 ( 36) link_NAG-ASN : bond 0.00328 / 0.23 ( 9) link_NAG-ASN : angle 2.53339 / 1.49 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8081 (m-30) cc_final: 0.7826 (m-30) REVERT: B 49 VAL cc_start: 0.8880 (t) cc_final: 0.8601 (p) REVERT: B 54 ASP cc_start: 0.8058 (m-30) cc_final: 0.7780 (m-30) REVERT: B 66 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8405 (mtmt) REVERT: B 93 GLU cc_start: 0.8849 (pt0) cc_final: 0.8597 (pt0) REVERT: B 95 GLU cc_start: 0.8315 (tt0) cc_final: 0.8004 (tt0) REVERT: B 191 LYS cc_start: 0.8038 (mppt) cc_final: 0.7778 (mmtm) REVERT: B 553 LEU cc_start: 0.8232 (mt) cc_final: 0.7974 (mp) REVERT: B 572 ASP cc_start: 0.8167 (m-30) cc_final: 0.7824 (m-30) REVERT: C 49 VAL cc_start: 0.8888 (t) cc_final: 0.8627 (p) REVERT: C 51 LYS cc_start: 0.8903 (mttm) cc_final: 0.8514 (mtmm) REVERT: C 54 ASP cc_start: 0.8225 (m-30) cc_final: 0.7942 (t0) REVERT: C 119 SER cc_start: 0.8999 (t) cc_final: 0.8711 (p) REVERT: C 538 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7890 (mtp-110) REVERT: C 572 ASP cc_start: 0.8259 (m-30) cc_final: 0.7668 (m-30) outliers start: 13 outliers final: 13 residues processed: 188 average time/residue: 0.1311 time to fit residues: 29.9964 Evaluate side-chains 192 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087003 restraints weight = 11123.965| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.56 r_work: 0.3018 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7056 Z= 0.200 Angle : 0.665 9.449 9597 Z= 0.325 Chirality : 0.046 0.328 1176 Planarity : 0.004 0.036 1140 Dihedral : 5.534 25.145 1467 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.27 % Allowed : 17.02 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.28), residues: 786 helix: -0.18 (0.37), residues: 189 sheet: -0.05 (0.33), residues: 243 loop : -1.01 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 207 TYR 0.009 0.001 TYR C 563 PHE 0.019 0.002 PHE A 26 TRP 0.009 0.001 TRP A 206 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 7020) covalent geometry : angle 0.63846 / 0.32 ( 9495) SS BOND : bond 0.00053 / 0.03 ( 6) SS BOND : angle 0.46276 / 0.27 ( 12) hydrogen bonds : bond 0.04465 / 2.92 ( 215) hydrogen bonds : angle 4.41832 / 3.00 ( 639) link_ALPHA1-3 : bond 0.00686 / 0.48 ( 6) link_ALPHA1-3 : angle 1.66142 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00378 / 0.21 ( 3) link_ALPHA1-6 : angle 1.66284 / 1.12 ( 9) link_BETA1-4 : bond 0.00380 / 0.25 ( 12) link_BETA1-4 : angle 1.82020 / 1.17 ( 36) link_NAG-ASN : bond 0.00420 / 0.29 ( 9) link_NAG-ASN : angle 2.56298 / 1.51 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.16 seconds wall clock time: 31 minutes 26.99 seconds (1886.99 seconds total)