Starting phenix.real_space_refine on Wed Jun 3 15:04:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opr_70722/06_2026/9opr_70722.map" } resolution = 3.2 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= 0.050 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 37 5.16 5 C 4171 2.51 5 N 1134 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 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6517 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2496 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 9, 'ASN:plan1': 6, 'TYR:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "H" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1543 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1560 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 852 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.83, per 1000 atoms: 0.28 Number of scatterers: 6517 At special positions: 0 Unit cell: (74.184, 77.556, 131.508, 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 37 16.00 O 1175 8.00 N 1134 7.00 C 4171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 465 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 25 " - pdb=" SG CYS N 99 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 213 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 363.7 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 18 sheets defined 10.5% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.628A pdb=" N GLY A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 477 through 491 removed outlier: 5.033A pdb=" N ASP A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.718A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.624A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 192 through 196 removed outlier: 3.545A pdb=" N LEU H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.633A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 68 removed outlier: 3.734A pdb=" N GLN N 68 " --> pdb=" O ASP N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 65 through 68' Processing helix chain 'N' and resid 90 through 94 removed outlier: 3.857A pdb=" N THR N 94 " --> pdb=" O PRO N 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 152 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 200 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 212 Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.594A pdb=" N CYS A 426 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A 473 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 445 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 382 " --> pdb=" O PRO A 444 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 448 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 378 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 275 removed outlier: 3.748A pdb=" N CYS A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 275 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 348 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A 331 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 350 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.873A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.428A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR H 106 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.145A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.145A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 157 through 161 removed outlier: 4.361A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.963A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.619A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.949A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'N' and resid 6 through 10 Processing sheet with id=AB8, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.182A pdb=" N GLY N 13 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA N 36 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET N 37 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL N 53 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP N 39 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.182A pdb=" N GLY N 13 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR N 113 " --> pdb=" O ILE N 101 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 672 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: 1.13 Time building geometry restraints manager: 0.74 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: 2107 1.34 - 1.46: 1633 1.46 - 1.58: 2857 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6647 Sorted by residual: bond pdb=" C TYR L 140 " pdb=" N PRO L 141 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.94e+00 bond pdb=" N GLY A 282 " pdb=" CA GLY A 282 " ideal model delta sigma weight residual 1.442 1.450 -0.008 7.70e-03 1.69e+04 1.10e+00 bond pdb=" CB VAL N 51 " pdb=" CG2 VAL N 51 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.64e-01 bond pdb=" CB ARG N 41 " pdb=" CG ARG N 41 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.43e-01 bond pdb=" CB VAL H 48 " pdb=" CG2 VAL H 48 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.14e-01 ... (remaining 6642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 8828 1.35 - 2.71: 199 2.71 - 4.06: 52 4.06 - 5.41: 7 5.41 - 6.77: 1 Bond angle restraints: 9087 Sorted by residual: angle pdb=" N LYS H 43 " pdb=" CA LYS H 43 " pdb=" C LYS H 43 " ideal model delta sigma weight residual 114.56 110.09 4.47 1.27e+00 6.20e-01 1.24e+01 angle pdb=" CA GLY A 282 " pdb=" C GLY A 282 " pdb=" N GLY A 283 " ideal model delta sigma weight residual 114.65 117.09 -2.44 9.20e-01 1.18e+00 7.03e+00 angle pdb=" C TRP H 102 " pdb=" N VAL H 103 " pdb=" CA VAL H 103 " ideal model delta sigma weight residual 121.97 126.60 -4.63 1.80e+00 3.09e-01 6.61e+00 angle pdb=" C TYR A 414 " pdb=" N VAL A 415 " pdb=" CA VAL A 415 " ideal model delta sigma weight residual 122.97 120.71 2.26 9.80e-01 1.04e+00 5.31e+00 angle pdb=" C LEU H 145 " pdb=" N GLY H 146 " pdb=" CA GLY H 146 " ideal model delta sigma weight residual 120.51 116.84 3.67 1.63e+00 3.76e-01 5.06e+00 ... (remaining 9082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 3658 17.09 - 34.18: 169 34.18 - 51.27: 36 51.27 - 68.36: 21 68.36 - 85.45: 5 Dihedral angle restraints: 3889 sinusoidal: 1341 harmonic: 2548 Sorted by residual: dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual 93.00 53.95 39.05 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CA ASN L 137 " pdb=" C ASN L 137 " pdb=" N ASN L 138 " pdb=" CA ASN L 138 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual -180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 610 0.033 - 0.066: 257 0.066 - 0.100: 87 0.100 - 0.133: 48 0.133 - 0.166: 4 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA TYR L 140 " pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CB TYR L 140 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1003 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A 422 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO L 80 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 304 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 305 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.018 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2529 2.92 - 3.41: 5415 3.41 - 3.91: 10183 3.91 - 4.40: 11752 4.40 - 4.90: 20859 Nonbonded interactions: 50738 Sorted by model distance: nonbonded pdb=" O HOH A 610 " pdb=" O HOH H 305 " model vdw 2.425 3.040 nonbonded pdb=" NH2 ARG L 61 " pdb=" OD1 ASP L 82 " model vdw 2.432 3.120 nonbonded pdb=" O HOH A 614 " pdb=" O HOH A 615 " model vdw 2.445 3.040 nonbonded pdb=" O GLN A 270 " pdb=" O HOH A 601 " model vdw 2.465 3.040 nonbonded pdb=" OG SER A 460 " pdb=" O HOH A 602 " model vdw 2.469 3.040 ... (remaining 50733 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=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: 9.280 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.004 0.031 6661 Z= 0.151 Angle : 0.554 6.767 9117 Z= 0.305 Chirality : 0.045 0.166 1006 Planarity : 0.004 0.036 1176 Dihedral : 11.959 85.451 2229 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.47 (0.29), residues: 874 helix: -0.23 (0.73), residues: 43 sheet: 1.40 (0.27), residues: 355 loop : 0.90 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 142 TYR 0.017 0.002 TYR L 91 PHE 0.014 0.002 PHE L 98 TRP 0.016 0.001 TRP H 110 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6647) covalent geometry : angle 0.55062 / 0.30 ( 9087) SS BOND : bond 0.00345 / 0.26 ( 12) SS BOND : angle 1.18890 / 0.77 ( 24) hydrogen bonds : bond 0.13988 / 9.26 ( 251) hydrogen bonds : angle 7.35249 / 5.31 ( 672) link_BETA1-4 : bond 0.00448 / 0.28 ( 1) link_BETA1-4 : angle 1.07758 / 0.48 ( 3) link_NAG-ASN : bond 0.00201 / 0.13 ( 1) link_NAG-ASN : angle 0.73283 / 0.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0952 time to fit residues: 7.1926 Evaluate side-chains 51 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN N 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100409 restraints weight = 7953.265| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.61 r_work: 0.2976 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6661 Z= 0.121 Angle : 0.499 6.616 9117 Z= 0.267 Chirality : 0.044 0.147 1006 Planarity : 0.004 0.033 1176 Dihedral : 4.020 17.797 998 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.53 % Allowed : 4.93 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.53 (0.29), residues: 874 helix: 0.12 (0.76), residues: 43 sheet: 1.48 (0.28), residues: 340 loop : 0.90 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.014 0.001 TYR L 91 PHE 0.014 0.001 PHE N 50 TRP 0.011 0.001 TRP H 110 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 6647) covalent geometry : angle 0.49716 / 0.27 ( 9087) SS BOND : bond 0.00291 / 0.22 ( 12) SS BOND : angle 0.92891 / 0.66 ( 24) hydrogen bonds : bond 0.03125 / 2.05 ( 251) hydrogen bonds : angle 5.68921 / 4.06 ( 672) link_BETA1-4 : bond 0.00415 / 0.26 ( 1) link_BETA1-4 : angle 0.97508 / 0.48 ( 3) link_NAG-ASN : bond 0.00184 / 0.11 ( 1) link_NAG-ASN : angle 0.96358 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.204 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.1131 time to fit residues: 9.1688 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS A 307 HIS N 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098974 restraints weight = 7884.998| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.57 r_work: 0.2939 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6661 Z= 0.133 Angle : 0.497 5.950 9117 Z= 0.264 Chirality : 0.044 0.149 1006 Planarity : 0.004 0.030 1176 Dihedral : 4.000 17.943 998 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.58 % Allowed : 5.11 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.46 (0.29), residues: 874 helix: 0.19 (0.75), residues: 43 sheet: 1.45 (0.28), residues: 340 loop : 0.82 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 48 TYR 0.014 0.002 TYR L 91 PHE 0.015 0.002 PHE N 50 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 6647) covalent geometry : angle 0.49449 / 0.26 ( 9087) SS BOND : bond 0.00323 / 0.25 ( 12) SS BOND : angle 0.91122 / 0.62 ( 24) hydrogen bonds : bond 0.02949 / 1.94 ( 251) hydrogen bonds : angle 5.37326 / 3.83 ( 672) link_BETA1-4 : bond 0.00422 / 0.26 ( 1) link_BETA1-4 : angle 0.94929 / 0.48 ( 3) link_NAG-ASN : bond 0.00168 / 0.10 ( 1) link_NAG-ASN : angle 1.06783 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.239 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0943 time to fit residues: 8.5817 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 56 optimal weight: 0.0050 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098835 restraints weight = 8000.320| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.59 r_work: 0.2939 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6661 Z= 0.127 Angle : 0.483 5.584 9117 Z= 0.256 Chirality : 0.044 0.146 1006 Planarity : 0.003 0.030 1176 Dihedral : 3.929 18.261 998 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 6.16 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.38 (0.29), residues: 874 helix: 0.25 (0.75), residues: 44 sheet: 1.32 (0.27), residues: 361 loop : 0.79 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 48 TYR 0.014 0.001 TYR L 91 PHE 0.014 0.001 PHE N 50 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6647) covalent geometry : angle 0.48121 / 0.26 ( 9087) SS BOND : bond 0.00316 / 0.24 ( 12) SS BOND : angle 0.82443 / 0.57 ( 24) hydrogen bonds : bond 0.02746 / 1.81 ( 251) hydrogen bonds : angle 5.25780 / 3.75 ( 672) link_BETA1-4 : bond 0.00354 / 0.22 ( 1) link_BETA1-4 : angle 0.88920 / 0.44 ( 3) link_NAG-ASN : bond 0.00188 / 0.12 ( 1) link_NAG-ASN : angle 1.10319 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.178 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.0848 time to fit residues: 7.6274 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098166 restraints weight = 8043.021| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.60 r_work: 0.2928 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6661 Z= 0.137 Angle : 0.494 5.498 9117 Z= 0.261 Chirality : 0.044 0.147 1006 Planarity : 0.003 0.030 1176 Dihedral : 3.951 18.454 998 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 6.69 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.32 (0.29), residues: 874 helix: 0.29 (0.75), residues: 44 sheet: 1.30 (0.27), residues: 360 loop : 0.73 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 48 TYR 0.015 0.001 TYR L 91 PHE 0.015 0.001 PHE N 50 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 6647) covalent geometry : angle 0.48959 / 0.26 ( 9087) SS BOND : bond 0.00437 / 0.34 ( 12) SS BOND : angle 1.27497 / 0.86 ( 24) hydrogen bonds : bond 0.02774 / 1.82 ( 251) hydrogen bonds : angle 5.26368 / 3.75 ( 672) link_BETA1-4 : bond 0.00438 / 0.27 ( 1) link_BETA1-4 : angle 0.91332 / 0.46 ( 3) link_NAG-ASN : bond 0.00192 / 0.12 ( 1) link_NAG-ASN : angle 1.15731 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.207 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.0949 time to fit residues: 8.1173 Evaluate side-chains 65 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098100 restraints weight = 7920.791| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.52 r_work: 0.2895 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6661 Z= 0.129 Angle : 0.487 5.425 9117 Z= 0.257 Chirality : 0.044 0.145 1006 Planarity : 0.003 0.029 1176 Dihedral : 3.910 18.389 998 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.76 % Allowed : 7.04 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.27 (0.29), residues: 874 helix: 0.48 (0.76), residues: 44 sheet: 1.26 (0.27), residues: 351 loop : 0.69 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 48 TYR 0.014 0.001 TYR L 91 PHE 0.014 0.001 PHE N 50 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6647) covalent geometry : angle 0.48427 / 0.26 ( 9087) SS BOND : bond 0.00349 / 0.27 ( 12) SS BOND : angle 1.04642 / 0.69 ( 24) hydrogen bonds : bond 0.02695 / 1.78 ( 251) hydrogen bonds : angle 5.19955 / 3.71 ( 672) link_BETA1-4 : bond 0.00379 / 0.24 ( 1) link_BETA1-4 : angle 0.86816 / 0.44 ( 3) link_NAG-ASN : bond 0.00184 / 0.11 ( 1) link_NAG-ASN : angle 1.10550 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.243 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.0999 time to fit residues: 9.2780 Evaluate side-chains 70 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 80 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 81 optimal weight: 0.0270 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100250 restraints weight = 7866.832| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.49 r_work: 0.2912 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6661 Z= 0.082 Angle : 0.454 5.895 9117 Z= 0.239 Chirality : 0.043 0.135 1006 Planarity : 0.003 0.029 1176 Dihedral : 3.730 17.906 998 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.58 % Allowed : 7.22 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.39 (0.29), residues: 874 helix: 0.75 (0.78), residues: 44 sheet: 1.48 (0.29), residues: 325 loop : 0.67 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 409 TYR 0.012 0.001 TYR L 91 PHE 0.008 0.001 PHE N 50 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 ( 6647) covalent geometry : angle 0.45210 / 0.24 ( 9087) SS BOND : bond 0.00258 / 0.20 ( 12) SS BOND : angle 0.75448 / 0.52 ( 24) hydrogen bonds : bond 0.02379 / 1.57 ( 251) hydrogen bonds : angle 4.95961 / 3.54 ( 672) link_BETA1-4 : bond 0.00302 / 0.19 ( 1) link_BETA1-4 : angle 0.83567 / 0.44 ( 3) link_NAG-ASN : bond 0.00151 / 0.09 ( 1) link_NAG-ASN : angle 0.92646 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.241 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.0927 time to fit residues: 8.4168 Evaluate side-chains 69 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096237 restraints weight = 7994.439| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.52 r_work: 0.2858 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6661 Z= 0.184 Angle : 0.531 7.058 9117 Z= 0.280 Chirality : 0.045 0.154 1006 Planarity : 0.004 0.031 1176 Dihedral : 4.073 19.049 998 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.41 % Allowed : 7.57 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.18 (0.29), residues: 874 helix: 0.58 (0.76), residues: 44 sheet: 1.20 (0.28), residues: 352 loop : 0.61 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 470 TYR 0.017 0.002 TYR L 91 PHE 0.017 0.002 PHE N 50 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.18 ( 6647) covalent geometry : angle 0.52779 / 0.28 ( 9087) SS BOND : bond 0.00415 / 0.32 ( 12) SS BOND : angle 1.09731 / 0.73 ( 24) hydrogen bonds : bond 0.03010 / 1.99 ( 251) hydrogen bonds : angle 5.36992 / 3.83 ( 672) link_BETA1-4 : bond 0.00373 / 0.23 ( 1) link_BETA1-4 : angle 0.86910 / 0.43 ( 3) link_NAG-ASN : bond 0.00178 / 0.11 ( 1) link_NAG-ASN : angle 1.31495 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.192 Fit side-chains REVERT: A 470 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7659 (mpt180) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.0797 time to fit residues: 7.3022 Evaluate side-chains 67 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 80 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099309 restraints weight = 7911.482| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.50 r_work: 0.2888 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6661 Z= 0.161 Angle : 0.518 6.927 9117 Z= 0.272 Chirality : 0.045 0.149 1006 Planarity : 0.004 0.033 1176 Dihedral : 4.055 19.117 998 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.41 % Allowed : 7.92 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.10 (0.29), residues: 874 helix: 0.60 (0.77), residues: 44 sheet: 1.15 (0.28), residues: 352 loop : 0.54 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 48 TYR 0.016 0.002 TYR L 91 PHE 0.017 0.002 PHE N 50 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 6647) covalent geometry : angle 0.51553 / 0.27 ( 9087) SS BOND : bond 0.00387 / 0.30 ( 12) SS BOND : angle 1.01062 / 0.67 ( 24) hydrogen bonds : bond 0.02888 / 1.91 ( 251) hydrogen bonds : angle 5.32457 / 3.80 ( 672) link_BETA1-4 : bond 0.00348 / 0.22 ( 1) link_BETA1-4 : angle 0.84529 / 0.42 ( 3) link_NAG-ASN : bond 0.00188 / 0.12 ( 1) link_NAG-ASN : angle 1.27388 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.177 Fit side-chains REVERT: A 470 ARG cc_start: 0.8110 (mpt180) cc_final: 0.7694 (mpt180) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.0844 time to fit residues: 7.3552 Evaluate side-chains 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 80 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099550 restraints weight = 7818.949| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.46 r_work: 0.2883 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6661 Z= 0.160 Angle : 0.512 6.903 9117 Z= 0.269 Chirality : 0.045 0.149 1006 Planarity : 0.004 0.034 1176 Dihedral : 4.057 18.926 998 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.23 % Allowed : 8.45 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.08 (0.29), residues: 874 helix: 0.64 (0.77), residues: 44 sheet: 1.13 (0.28), residues: 352 loop : 0.52 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.016 0.002 TYR L 91 PHE 0.017 0.002 PHE N 50 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 6647) covalent geometry : angle 0.50929 / 0.27 ( 9087) SS BOND : bond 0.00386 / 0.30 ( 12) SS BOND : angle 0.99863 / 0.67 ( 24) hydrogen bonds : bond 0.02876 / 1.90 ( 251) hydrogen bonds : angle 5.32201 / 3.80 ( 672) link_BETA1-4 : bond 0.00368 / 0.23 ( 1) link_BETA1-4 : angle 0.84216 / 0.42 ( 3) link_NAG-ASN : bond 0.00171 / 0.11 ( 1) link_NAG-ASN : angle 1.28121 / 0.60 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.242 Fit side-chains REVERT: A 470 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7724 (mpt180) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.0977 time to fit residues: 8.2186 Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 0.0870 chunk 58 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 overall best weight: 0.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103360 restraints weight = 7766.453| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.49 r_work: 0.2912 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6661 Z= 0.078 Angle : 0.447 5.438 9117 Z= 0.235 Chirality : 0.042 0.132 1006 Planarity : 0.003 0.031 1176 Dihedral : 3.678 17.740 998 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.06 % Allowed : 8.63 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.30 (0.29), residues: 874 helix: 1.00 (0.80), residues: 44 sheet: 1.36 (0.29), residues: 327 loop : 0.63 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.010 0.001 TYR L 91 PHE 0.008 0.001 PHE N 50 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 ( 6647) covalent geometry : angle 0.44559 / 0.23 ( 9087) SS BOND : bond 0.00240 / 0.18 ( 12) SS BOND : angle 0.64427 / 0.45 ( 24) hydrogen bonds : bond 0.02281 / 1.51 ( 251) hydrogen bonds : angle 4.85531 / 3.47 ( 672) link_BETA1-4 : bond 0.00192 / 0.12 ( 1) link_BETA1-4 : angle 0.78989 / 0.41 ( 3) link_NAG-ASN : bond 0.00153 / 0.10 ( 1) link_NAG-ASN : angle 0.84325 / 0.39 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.68 seconds wall clock time: 32 minutes 51.70 seconds (1971.70 seconds total)