Starting phenix.real_space_refine on Tue Aug 4 17:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xtu_67251/08_2026/9xtu_67251.map" } resolution = 2.96 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= 0.000 sd= 0.023 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 23 5.16 5 C 3246 2.51 5 N 866 2.21 5 O 1026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5161 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1489 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 5 Chain: "L" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1210 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain breaks: 4 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 2 Chain: "E" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 753 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain breaks: 3 Chain: "C" 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 Time building chain proxies: 0.89, per 1000 atoms: 0.17 Number of scatterers: 5161 At special positions: 0 Unit cell: (64.17, 66.96, 131.13, 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 23 16.00 O 1026 8.00 N 866 7.00 C 3246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 117 " distance=2.03 Simple disulfide: pdb=" SG CYS H 72 " - pdb=" SG CYS H 122 " distance=2.02 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS H 225 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 109 " - pdb=" SG CYS E 121 " 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 NAG-ASN " NAG C 701 " - " ASN C 556 " " NAG C 702 " - " ASN C 514 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 112.0 milliseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 18 sheets defined 5.4% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.983A pdb=" N VAL H 50 " --> pdb=" O THR H 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.602A pdb=" N ASP L 102 " --> pdb=" O GLN L 99 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU L 103 " --> pdb=" O ALA L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 103' Processing helix chain 'L' and resid 202 through 208 removed outlier: 3.688A pdb=" N LYS L 207 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER L 208 " --> pdb=" O SER L 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 579 removed outlier: 4.164A pdb=" N VAL C 579 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.858A pdb=" N GLU E 103 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.717A pdb=" N VAL H 31 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR H 54 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL H 53 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.717A pdb=" N VAL H 31 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG H 119 " --> pdb=" O ASN H 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 149 through 152 removed outlier: 6.277A pdb=" N TYR H 205 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER H 206 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL H 198 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AA6, first strand: chain 'H' and resid 180 through 182 removed outlier: 3.514A pdb=" N VAL H 236 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 22 through 23 Processing sheet with id=AA8, first strand: chain 'L' and resid 27 through 31 removed outlier: 6.617A pdb=" N ARG L 28 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU L 127 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 30 " --> pdb=" O LEU L 127 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 27 through 31 removed outlier: 6.617A pdb=" N ARG L 28 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU L 127 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 30 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 136 through 139 Processing sheet with id=AB2, first strand: chain 'L' and resid 136 through 139 Processing sheet with id=AB3, first strand: chain 'C' and resid 526 through 536 removed outlier: 5.286A pdb=" N ASN C 528 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER C 520 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER C 532 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER C 518 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 534 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 516 " --> pdb=" O THR C 534 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 536 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN C 514 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 550 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.459A pdb=" N LYS C 587 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 618 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 600 " --> pdb=" O ASN C 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 23 through 26 Processing sheet with id=AB6, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.940A pdb=" N LEU D 128 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 22 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.275A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 86 178 hydrogen bonds defined for protein. 426 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: 0.88 Time building geometry restraints manager: 0.34 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: 1633 1.34 - 1.46: 1125 1.46 - 1.57: 2485 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5270 Sorted by residual: bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C VAL H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 bond pdb=" C GLU H 177 " pdb=" N PRO H 178 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.19e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CG LEU C 604 " pdb=" CD1 LEU C 604 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 ... (remaining 5265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 6965 2.06 - 4.12: 167 4.12 - 6.17: 20 6.17 - 8.23: 9 8.23 - 10.29: 4 Bond angle restraints: 7165 Sorted by residual: angle pdb=" N VAL D 120 " pdb=" CA VAL D 120 " pdb=" C VAL D 120 " ideal model delta sigma weight residual 112.43 103.24 9.19 9.20e-01 1.18e+00 9.98e+01 angle pdb=" C ASN E 70 " pdb=" N THR E 71 " pdb=" CA THR E 71 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 angle pdb=" N GLY H 29 " pdb=" CA GLY H 29 " pdb=" C GLY H 29 " ideal model delta sigma weight residual 110.20 114.58 -4.38 1.32e+00 5.74e-01 1.10e+01 angle pdb=" C SER E 115 " pdb=" N LYS E 116 " pdb=" CA LYS E 116 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TRP H 183 " pdb=" N ASN H 184 " pdb=" CA ASN H 184 " ideal model delta sigma weight residual 121.26 126.27 -5.01 1.59e+00 3.96e-01 9.91e+00 ... (remaining 7160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 2818 15.95 - 31.90: 248 31.90 - 47.85: 42 47.85 - 63.79: 12 63.79 - 79.74: 5 Dihedral angle restraints: 3125 sinusoidal: 1190 harmonic: 1935 Sorted by residual: dihedral pdb=" CB CYS D 41 " pdb=" SG CYS D 41 " pdb=" SG CYS D 115 " pdb=" CB CYS D 115 " ideal model delta sinusoidal sigma weight residual 93.00 158.81 -65.81 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA ASN H 71 " pdb=" C ASN H 71 " pdb=" N CYS H 72 " pdb=" CA CYS H 72 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLN L 58 " pdb=" C GLN L 58 " pdb=" N THR L 59 " pdb=" CA THR L 59 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 3122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 779 0.106 - 0.213: 45 0.213 - 0.319: 3 0.319 - 0.425: 0 0.425 - 0.531: 1 Chirality restraints: 828 Sorted by residual: chirality pdb=" CB ILE E 119 " pdb=" CA ILE E 119 " pdb=" CG1 ILE E 119 " pdb=" CG2 ILE E 119 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CB ILE E 36 " pdb=" CA ILE E 36 " pdb=" CG1 ILE E 36 " pdb=" CG2 ILE E 36 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 601 " pdb=" CA ILE C 601 " pdb=" CG1 ILE C 601 " pdb=" CG2 ILE C 601 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 825 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 601 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ILE C 601 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE C 601 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP C 602 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG L 74 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO L 75 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO L 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 75 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 78 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO E 79 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 79 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 79 " -0.031 5.00e-02 4.00e+02 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1711 2.85 - 3.36: 4114 3.36 - 3.87: 8487 3.87 - 4.39: 9669 4.39 - 4.90: 17042 Nonbonded interactions: 41023 Sorted by model distance: nonbonded pdb=" OG SER E 83 " pdb=" OG1 THR E 94 " model vdw 2.332 3.040 nonbonded pdb=" OG SER C 586 " pdb=" OG1 THR C 623 " model vdw 2.333 3.040 nonbonded pdb=" OE1 GLU E 25 " pdb=" OG1 THR E 39 " model vdw 2.337 3.040 nonbonded pdb=" NE ARG D 57 " pdb=" OE2 GLU D 65 " model vdw 2.343 3.120 nonbonded pdb=" O SER C 584 " pdb=" OG SER C 584 " model vdw 2.347 3.040 ... (remaining 41018 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.020 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 0.048 5281 Z= 0.193 Angle : 0.791 10.289 7189 Z= 0.424 Chirality : 0.055 0.531 828 Planarity : 0.006 0.062 908 Dihedral : 12.663 79.744 1858 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.95 (0.34), residues: 645 helix: None (None), residues: 0 sheet: -0.36 (0.30), residues: 295 loop : -0.80 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 28 TYR 0.019 0.002 TYR L 69 PHE 0.015 0.002 PHE C 615 TRP 0.009 0.002 TRP D 66 HIS 0.002 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 5270) covalent geometry : angle 0.78203 / 0.42 ( 7165) SS BOND : bond 0.00482 / 0.23 ( 9) SS BOND : angle 1.85664 / 1.03 ( 18) hydrogen bonds : bond 0.18597 / 13.45 ( 168) hydrogen bonds : angle 8.84965 / 6.19 ( 426) link_NAG-ASN : bond 0.00059 / 0.03 ( 2) link_NAG-ASN : angle 3.00025 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3585 time to fit residues: 26.6128 Evaluate side-chains 56 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.208759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172990 restraints weight = 4634.442| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.14 r_work: 0.3941 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5281 Z= 0.117 Angle : 0.567 6.712 7189 Z= 0.288 Chirality : 0.044 0.230 828 Planarity : 0.005 0.050 908 Dihedral : 5.440 59.960 763 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.75 % Allowed : 8.22 % Favored : 90.03 % 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: -0.84 (0.34), residues: 645 helix: -3.20 (1.42), residues: 7 sheet: -0.33 (0.29), residues: 305 loop : -0.60 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 81 TYR 0.012 0.001 TYR L 69 PHE 0.012 0.001 PHE H 46 TRP 0.008 0.001 TRP D 66 HIS 0.003 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5270) covalent geometry : angle 0.56059 / 0.29 ( 7165) SS BOND : bond 0.00308 / 0.14 ( 9) SS BOND : angle 1.00280 / 0.54 ( 18) hydrogen bonds : bond 0.03232 / 2.28 ( 168) hydrogen bonds : angle 6.18376 / 4.28 ( 426) link_NAG-ASN : bond 0.00137 / 0.07 ( 2) link_NAG-ASN : angle 2.49702 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.188 Fit side-chains REVERT: H 114 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: H 181 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6429 (ptt) REVERT: H 210 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5745 (ttt) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.2931 time to fit residues: 20.0113 Evaluate side-chains 62 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 GLN ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165627 restraints weight = 4647.166| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.15 r_work: 0.3863 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5281 Z= 0.167 Angle : 0.610 7.892 7189 Z= 0.306 Chirality : 0.045 0.205 828 Planarity : 0.005 0.048 908 Dihedral : 5.410 56.049 763 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.50 % Allowed : 11.19 % Favored : 85.31 % 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: -0.77 (0.34), residues: 645 helix: -2.58 (1.92), residues: 7 sheet: -0.37 (0.29), residues: 316 loop : -0.47 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 81 TYR 0.014 0.002 TYR L 69 PHE 0.013 0.002 PHE C 585 TRP 0.013 0.002 TRP D 66 HIS 0.003 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 5270) covalent geometry : angle 0.60415 / 0.30 ( 7165) SS BOND : bond 0.00468 / 0.22 ( 9) SS BOND : angle 0.98012 / 0.50 ( 18) hydrogen bonds : bond 0.03421 / 2.33 ( 168) hydrogen bonds : angle 5.86930 / 4.02 ( 426) link_NAG-ASN : bond 0.00342 / 0.17 ( 2) link_NAG-ASN : angle 2.66285 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.108 Fit side-chains REVERT: H 64 LEU cc_start: 0.7216 (mt) cc_final: 0.6891 (mt) REVERT: H 181 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6562 (ptt) REVERT: H 210 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6168 (ttt) REVERT: E 74 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6594 (mtp180) REVERT: E 90 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5836 (mtp85) outliers start: 20 outliers final: 13 residues processed: 65 average time/residue: 0.2770 time to fit residues: 19.2664 Evaluate side-chains 72 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 90 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.199067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166022 restraints weight = 4757.220| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.10 r_work: 0.3856 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5281 Z= 0.184 Angle : 0.623 10.321 7189 Z= 0.315 Chirality : 0.045 0.210 828 Planarity : 0.005 0.047 908 Dihedral : 5.238 45.527 763 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.55 % Allowed : 12.59 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.34), residues: 645 helix: -2.33 (2.02), residues: 7 sheet: -0.45 (0.29), residues: 316 loop : -0.57 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 57 TYR 0.013 0.002 TYR L 69 PHE 0.014 0.002 PHE C 585 TRP 0.012 0.002 TRP D 66 HIS 0.003 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 ( 5270) covalent geometry : angle 0.61732 / 0.31 ( 7165) SS BOND : bond 0.00474 / 0.23 ( 9) SS BOND : angle 0.88042 / 0.44 ( 18) hydrogen bonds : bond 0.03335 / 2.29 ( 168) hydrogen bonds : angle 5.81731 / 3.97 ( 426) link_NAG-ASN : bond 0.00225 / 0.11 ( 2) link_NAG-ASN : angle 2.81216 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.176 Fit side-chains REVERT: H 181 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6714 (ptt) REVERT: H 210 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.6010 (ttt) REVERT: L 95 ILE cc_start: 0.5499 (mt) cc_final: 0.5230 (mp) REVERT: E 74 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6618 (mtp180) REVERT: E 90 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.5913 (mtp85) outliers start: 26 outliers final: 17 residues processed: 72 average time/residue: 0.2730 time to fit residues: 21.1085 Evaluate side-chains 76 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 90 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.201206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168117 restraints weight = 4717.272| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.18 r_work: 0.3858 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5281 Z= 0.164 Angle : 0.599 9.119 7189 Z= 0.302 Chirality : 0.046 0.385 828 Planarity : 0.004 0.046 908 Dihedral : 4.896 32.168 763 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.90 % Allowed : 14.69 % Favored : 80.42 % 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: -0.97 (0.34), residues: 645 helix: -2.32 (1.83), residues: 7 sheet: -0.52 (0.28), residues: 316 loop : -0.61 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 114 TYR 0.013 0.002 TYR H 116 PHE 0.012 0.001 PHE C 585 TRP 0.010 0.002 TRP D 66 HIS 0.003 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 5270) covalent geometry : angle 0.59226 / 0.30 ( 7165) SS BOND : bond 0.00407 / 0.20 ( 9) SS BOND : angle 0.81687 / 0.42 ( 18) hydrogen bonds : bond 0.03160 / 2.15 ( 168) hydrogen bonds : angle 5.68653 / 3.88 ( 426) link_NAG-ASN : bond 0.00218 / 0.11 ( 2) link_NAG-ASN : angle 2.99119 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.189 Fit side-chains REVERT: H 181 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6880 (ptt) REVERT: D 106 ARG cc_start: 0.6974 (ptp90) cc_final: 0.6561 (ptp90) REVERT: E 74 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6658 (mtp180) REVERT: E 90 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5783 (mtp85) outliers start: 28 outliers final: 20 residues processed: 71 average time/residue: 0.2916 time to fit residues: 22.1155 Evaluate side-chains 76 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 90 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.199590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166410 restraints weight = 4842.753| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.12 r_work: 0.3863 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5281 Z= 0.165 Angle : 0.603 9.003 7189 Z= 0.304 Chirality : 0.045 0.330 828 Planarity : 0.004 0.045 908 Dihedral : 4.781 23.471 763 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.42 % Allowed : 14.86 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.34), residues: 645 helix: -2.38 (1.74), residues: 7 sheet: -0.53 (0.28), residues: 316 loop : -0.63 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.012 0.002 TYR H 116 PHE 0.012 0.001 PHE C 585 TRP 0.011 0.002 TRP D 66 HIS 0.002 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 5270) covalent geometry : angle 0.59512 / 0.30 ( 7165) SS BOND : bond 0.00415 / 0.20 ( 9) SS BOND : angle 0.82053 / 0.42 ( 18) hydrogen bonds : bond 0.03146 / 2.16 ( 168) hydrogen bonds : angle 5.62075 / 3.83 ( 426) link_NAG-ASN : bond 0.00150 / 0.08 ( 2) link_NAG-ASN : angle 3.23939 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: H 181 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6900 (ptt) REVERT: L 115 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6765 (pp) REVERT: D 106 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6637 (ptp90) REVERT: E 74 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6632 (mtp180) REVERT: E 90 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.5779 (mtp85) outliers start: 31 outliers final: 23 residues processed: 74 average time/residue: 0.2866 time to fit residues: 22.6447 Evaluate side-chains 80 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 90 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.204035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168961 restraints weight = 4728.174| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.07 r_work: 0.3893 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5281 Z= 0.109 Angle : 0.544 8.249 7189 Z= 0.277 Chirality : 0.043 0.291 828 Planarity : 0.004 0.044 908 Dihedral : 4.425 19.122 763 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.55 % Allowed : 16.43 % Favored : 79.02 % 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: -0.86 (0.34), residues: 645 helix: -2.32 (1.78), residues: 7 sheet: -0.40 (0.29), residues: 308 loop : -0.58 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 114 TYR 0.009 0.001 TYR E 69 PHE 0.009 0.001 PHE C 609 TRP 0.011 0.001 TRP D 66 HIS 0.002 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 5270) covalent geometry : angle 0.53811 / 0.28 ( 7165) SS BOND : bond 0.00206 / 0.10 ( 9) SS BOND : angle 0.63739 / 0.34 ( 18) hydrogen bonds : bond 0.02708 / 1.86 ( 168) hydrogen bonds : angle 5.28308 / 3.61 ( 426) link_NAG-ASN : bond 0.00089 / 0.04 ( 2) link_NAG-ASN : angle 2.74731 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: H 114 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7576 (ttm-80) REVERT: H 181 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6891 (ptt) REVERT: D 106 ARG cc_start: 0.6812 (ptp90) cc_final: 0.6451 (ptp90) REVERT: E 74 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6697 (mtp180) outliers start: 26 outliers final: 18 residues processed: 71 average time/residue: 0.3278 time to fit residues: 24.5927 Evaluate side-chains 73 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.0000 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167151 restraints weight = 4776.577| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.03 r_work: 0.3878 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5281 Z= 0.159 Angle : 0.586 8.160 7189 Z= 0.295 Chirality : 0.044 0.279 828 Planarity : 0.004 0.045 908 Dihedral : 4.623 22.322 763 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.90 % Allowed : 16.08 % Favored : 79.02 % 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: -0.89 (0.34), residues: 645 helix: -2.24 (1.71), residues: 7 sheet: -0.43 (0.28), residues: 317 loop : -0.58 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 114 TYR 0.014 0.002 TYR L 69 PHE 0.012 0.001 PHE C 585 TRP 0.008 0.002 TRP D 66 HIS 0.002 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 5270) covalent geometry : angle 0.57936 / 0.29 ( 7165) SS BOND : bond 0.00424 / 0.20 ( 9) SS BOND : angle 0.81278 / 0.42 ( 18) hydrogen bonds : bond 0.03015 / 2.06 ( 168) hydrogen bonds : angle 5.44331 / 3.70 ( 426) link_NAG-ASN : bond 0.00180 / 0.09 ( 2) link_NAG-ASN : angle 2.88590 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: H 181 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6915 (ptt) REVERT: L 115 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6809 (pp) REVERT: E 74 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6679 (mtp180) outliers start: 28 outliers final: 23 residues processed: 74 average time/residue: 0.3174 time to fit residues: 25.0269 Evaluate side-chains 78 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.203037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168236 restraints weight = 4736.083| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.07 r_work: 0.3889 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5281 Z= 0.116 Angle : 0.547 7.827 7189 Z= 0.277 Chirality : 0.043 0.271 828 Planarity : 0.004 0.044 908 Dihedral : 4.431 19.515 763 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.20 % Allowed : 16.78 % Favored : 79.02 % 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: -0.80 (0.34), residues: 645 helix: -2.06 (1.79), residues: 7 sheet: -0.35 (0.29), residues: 308 loop : -0.55 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 114 TYR 0.011 0.001 TYR L 69 PHE 0.009 0.001 PHE C 609 TRP 0.009 0.001 TRP D 66 HIS 0.002 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5270) covalent geometry : angle 0.54105 / 0.28 ( 7165) SS BOND : bond 0.00235 / 0.12 ( 9) SS BOND : angle 0.73237 / 0.39 ( 18) hydrogen bonds : bond 0.02738 / 1.85 ( 168) hydrogen bonds : angle 5.23452 / 3.57 ( 426) link_NAG-ASN : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : angle 2.69978 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: H 114 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7576 (ttm-80) REVERT: H 181 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6927 (ptt) REVERT: L 115 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6811 (pp) REVERT: E 74 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6707 (mtp180) outliers start: 24 outliers final: 19 residues processed: 69 average time/residue: 0.3586 time to fit residues: 26.3501 Evaluate side-chains 73 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.168486 restraints weight = 4797.924| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.10 r_work: 0.3890 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5281 Z= 0.149 Angle : 0.574 7.948 7189 Z= 0.290 Chirality : 0.044 0.264 828 Planarity : 0.004 0.045 908 Dihedral : 4.567 21.879 763 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.37 % Allowed : 17.31 % Favored : 78.32 % 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 (0.34), residues: 645 helix: -2.05 (1.77), residues: 7 sheet: -0.33 (0.29), residues: 308 loop : -0.60 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 114 TYR 0.013 0.002 TYR L 69 PHE 0.011 0.001 PHE C 585 TRP 0.007 0.002 TRP H 132 HIS 0.002 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5270) covalent geometry : angle 0.56806 / 0.29 ( 7165) SS BOND : bond 0.00354 / 0.18 ( 9) SS BOND : angle 0.79535 / 0.41 ( 18) hydrogen bonds : bond 0.02939 / 1.98 ( 168) hydrogen bonds : angle 5.34709 / 3.63 ( 426) link_NAG-ASN : bond 0.00172 / 0.09 ( 2) link_NAG-ASN : angle 2.77410 / 1.34 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: H 181 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6998 (ptt) REVERT: L 115 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6804 (pp) REVERT: E 74 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6662 (mtp180) outliers start: 25 outliers final: 22 residues processed: 70 average time/residue: 0.2992 time to fit residues: 22.2571 Evaluate side-chains 78 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 190 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 5 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.200266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.164956 restraints weight = 4797.191| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.08 r_work: 0.3859 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5281 Z= 0.151 Angle : 0.576 7.831 7189 Z= 0.291 Chirality : 0.044 0.268 828 Planarity : 0.004 0.045 908 Dihedral : 4.613 22.085 763 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.72 % Allowed : 16.96 % Favored : 78.32 % 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: -0.87 (0.34), residues: 645 helix: -1.92 (1.78), residues: 7 sheet: -0.36 (0.29), residues: 310 loop : -0.65 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 114 TYR 0.013 0.002 TYR L 69 PHE 0.011 0.001 PHE C 585 TRP 0.008 0.002 TRP H 132 HIS 0.002 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 5270) covalent geometry : angle 0.57035 / 0.29 ( 7165) SS BOND : bond 0.00351 / 0.18 ( 9) SS BOND : angle 0.79185 / 0.41 ( 18) hydrogen bonds : bond 0.02955 / 1.99 ( 168) hydrogen bonds : angle 5.38061 / 3.66 ( 426) link_NAG-ASN : bond 0.00172 / 0.09 ( 2) link_NAG-ASN : angle 2.78459 / 1.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.58 seconds wall clock time: 25 minutes 34.35 seconds (1534.35 seconds total)