Starting phenix.real_space_refine on Wed Jul 1 21:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2026/7ly0_23581.map" } resolution = 2.6 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= 0.039 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 10 5.16 5 C 1796 2.51 5 N 463 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 7 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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 chiralities: 2 Time building chain proxies: 0.83, per 1000 atoms: 0.30 Number of scatterers: 2805 At special positions: 0 Unit cell: (73.5, 71.4, 74.55, 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 10 16.00 O 536 8.00 N 463 7.00 C 1796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 100.5 milliseconds 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.185A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.544A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.002A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 225 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: 0.32 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 520 1.32 - 1.45: 807 1.45 - 1.57: 1528 1.57 - 1.70: 4 1.70 - 1.82: 13 Bond restraints: 2872 Sorted by residual: bond pdb=" N TRP H 104 " pdb=" CA TRP H 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB ILE A 235 " pdb=" CG1 ILE A 235 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG ASP A 138 " pdb=" OD1 ASP A 138 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.23e+00 ... (remaining 2867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 3280 1.46 - 2.92: 518 2.92 - 4.38: 68 4.38 - 5.84: 25 5.84 - 7.30: 14 Bond angle restraints: 3905 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.30e-01 1.88e+00 7.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.32 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.82 -6.79 9.90e-01 1.02e+00 4.71e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.92 127.22 -7.30 1.07e+00 8.73e-01 4.65e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.19 126.17 -6.98 1.06e+00 8.90e-01 4.33e+01 ... (remaining 3900 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1552 17.83 - 35.65: 35 35.65 - 53.48: 14 53.48 - 71.30: 3 71.30 - 89.12: 1 Dihedral angle restraints: 1605 sinusoidal: 588 harmonic: 1017 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.87 41.13 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 55.35 37.65 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.124: 104 0.124 - 0.186: 29 0.186 - 0.248: 16 0.248 - 0.309: 5 Chirality restraints: 450 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.24e+01 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.19e+01 chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.82e+00 ... (remaining 447 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.18e+00 pdb=" CG TYR L 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.024 2.00e-02 2.50e+03 2.31e-02 6.67e+00 pdb=" CG ASN A 122 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLU H 103 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP H 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1504 2.99 - 3.47: 2388 3.47 - 3.95: 4816 3.95 - 4.42: 5482 4.42 - 4.90: 8858 Nonbonded interactions: 23048 Sorted by model distance: nonbonded pdb=" NZ LYS A 77 " pdb=" O THR A 250 " model vdw 2.515 3.120 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 3.120 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 3.120 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 3.120 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 3.120 ... (remaining 23043 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: 4.190 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.630 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.067 2881 Z= 0.646 Angle : 1.198 7.298 3929 Z= 0.800 Chirality : 0.080 0.309 450 Planarity : 0.005 0.019 481 Dihedral : 9.792 89.124 946 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.29 % 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: 1.70 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.04 (0.39), residues: 154 loop : 1.42 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.035 0.004 TYR L 33 PHE 0.014 0.003 PHE A 175 TRP 0.014 0.004 TRP L 34 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.01191 / 0.63 ( 2872) covalent geometry : angle 1.18702 / 0.80 ( 3905) SS BOND : bond 0.00404 / 0.19 ( 3) SS BOND : angle 2.38100 / 1.35 ( 6) hydrogen bonds : bond 0.12230 / 8.34 ( 94) hydrogen bonds : angle 8.05201 / 5.36 ( 225) link_ALPHA1-4 : bond 0.06677 / 3.51 ( 1) link_ALPHA1-4 : angle 3.07699 / 1.62 ( 3) link_BETA1-4 : bond 0.06179 / 3.25 ( 1) link_BETA1-4 : angle 3.03880 / 1.59 ( 3) link_BETA1-6 : bond 0.04555 / 2.40 ( 1) link_BETA1-6 : angle 1.44181 / 0.78 ( 3) link_NAG-ASN : bond 0.05587 / 2.79 ( 3) link_NAG-ASN : angle 2.16031 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.100 Fit side-chains REVERT: A 19 THR cc_start: 0.7681 (m) cc_final: 0.7459 (m) REVERT: A 86 PHE cc_start: 0.8153 (t80) cc_final: 0.7943 (t80) REVERT: L 20 ILE cc_start: 0.7448 (mt) cc_final: 0.7151 (mp) REVERT: L 31 TYR cc_start: 0.8175 (m-80) cc_final: 0.7627 (m-80) REVERT: L 53 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7921 (mtm110) REVERT: L 86 TYR cc_start: 0.8811 (m-80) cc_final: 0.8570 (m-80) REVERT: L 98 VAL cc_start: 0.8630 (p) cc_final: 0.8395 (t) REVERT: H 18 LEU cc_start: 0.7209 (tt) cc_final: 0.7004 (tp) REVERT: H 27 PHE cc_start: 0.7322 (p90) cc_final: 0.6992 (p90) REVERT: H 45 LEU cc_start: 0.8886 (mt) cc_final: 0.8563 (mt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.3220 time to fit residues: 32.4678 Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.189317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183928 restraints weight = 2816.663| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.69 r_work: 0.3923 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2881 Z= 0.147 Angle : 0.571 5.905 3929 Z= 0.292 Chirality : 0.044 0.162 450 Planarity : 0.004 0.036 481 Dihedral : 4.577 16.068 384 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.50 % Allowed : 11.79 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.19 (0.40), residues: 152 loop : 1.28 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.009 0.001 TYR H 60 PHE 0.009 0.001 PHE A 133 TRP 0.008 0.001 TRP L 34 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 2872) covalent geometry : angle 0.55894 / 0.29 ( 3905) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 0.41301 / 0.24 ( 6) hydrogen bonds : bond 0.03479 / 2.43 ( 94) hydrogen bonds : angle 6.34437 / 4.27 ( 225) link_ALPHA1-4 : bond 0.01962 / 1.03 ( 1) link_ALPHA1-4 : angle 2.49515 / 1.15 ( 3) link_BETA1-4 : bond 0.00471 / 0.25 ( 1) link_BETA1-4 : angle 1.80517 / 0.88 ( 3) link_BETA1-6 : bond 0.00408 / 0.21 ( 1) link_BETA1-6 : angle 1.30187 / 0.65 ( 3) link_NAG-ASN : bond 0.00271 / 0.14 ( 3) link_NAG-ASN : angle 1.74528 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.103 Fit side-chains REVERT: A 19 THR cc_start: 0.8085 (m) cc_final: 0.7788 (m) REVERT: A 190 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6843 (mtt-85) REVERT: L 31 TYR cc_start: 0.8366 (m-80) cc_final: 0.7989 (m-80) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.3134 time to fit residues: 28.9822 Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.182232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.176881 restraints weight = 2825.545| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 0.67 r_work: 0.3821 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2881 Z= 0.217 Angle : 0.632 6.385 3929 Z= 0.325 Chirality : 0.046 0.163 450 Planarity : 0.005 0.044 481 Dihedral : 4.941 16.947 384 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.00 % Allowed : 12.86 % Favored : 82.14 % 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: 1.10 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.75 (0.40), residues: 153 loop : 0.90 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 72 TYR 0.011 0.002 TYR L 31 PHE 0.013 0.002 PHE A 175 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 2872) covalent geometry : angle 0.61558 / 0.32 ( 3905) SS BOND : bond 0.00054 / 0.03 ( 3) SS BOND : angle 2.01397 / 1.15 ( 6) hydrogen bonds : bond 0.03772 / 2.58 ( 94) hydrogen bonds : angle 6.26548 / 4.24 ( 225) link_ALPHA1-4 : bond 0.01863 / 0.98 ( 1) link_ALPHA1-4 : angle 2.32971 / 1.13 ( 3) link_BETA1-4 : bond 0.00388 / 0.20 ( 1) link_BETA1-4 : angle 1.50677 / 0.76 ( 3) link_BETA1-6 : bond 0.00162 / 0.09 ( 1) link_BETA1-6 : angle 1.09500 / 0.56 ( 3) link_NAG-ASN : bond 0.00156 / 0.08 ( 3) link_NAG-ASN : angle 2.13010 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.105 Fit side-chains REVERT: A 190 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6910 (mtt-85) REVERT: A 248 TYR cc_start: 0.8234 (t80) cc_final: 0.7941 (t80) REVERT: L 9 SER cc_start: 0.5512 (p) cc_final: 0.4910 (t) REVERT: L 16 GLN cc_start: 0.5997 (mt0) cc_final: 0.5438 (mp10) REVERT: L 31 TYR cc_start: 0.8576 (m-80) cc_final: 0.7932 (m-80) REVERT: L 104 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7820 (ttpp) REVERT: H 27 PHE cc_start: 0.7460 (p90) cc_final: 0.7249 (p90) REVERT: H 45 LEU cc_start: 0.8736 (mt) cc_final: 0.8524 (mt) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.3581 time to fit residues: 34.9103 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.1626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.183860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.178376 restraints weight = 2820.557| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 0.68 r_work: 0.3849 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2881 Z= 0.133 Angle : 0.556 5.270 3929 Z= 0.284 Chirality : 0.044 0.165 450 Planarity : 0.004 0.040 481 Dihedral : 4.564 14.942 384 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % Favored : 80.00 % 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 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.69 (0.40), residues: 155 loop : 0.75 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.010 0.001 TYR L 31 PHE 0.007 0.001 PHE L 99 TRP 0.004 0.001 TRP L 34 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 2872) covalent geometry : angle 0.53939 / 0.28 ( 3905) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 2.11073 / 1.20 ( 6) hydrogen bonds : bond 0.03217 / 2.24 ( 94) hydrogen bonds : angle 5.98643 / 4.05 ( 225) link_ALPHA1-4 : bond 0.01654 / 0.87 ( 1) link_ALPHA1-4 : angle 2.28770 / 1.10 ( 3) link_BETA1-4 : bond 0.00495 / 0.26 ( 1) link_BETA1-4 : angle 1.34689 / 0.64 ( 3) link_BETA1-6 : bond 0.00230 / 0.12 ( 1) link_BETA1-6 : angle 1.14053 / 0.57 ( 3) link_NAG-ASN : bond 0.00173 / 0.09 ( 3) link_NAG-ASN : angle 1.73493 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.106 Fit side-chains REVERT: A 190 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6919 (mtt-85) REVERT: A 248 TYR cc_start: 0.8175 (t80) cc_final: 0.7877 (t80) REVERT: L 9 SER cc_start: 0.5337 (p) cc_final: 0.4811 (t) REVERT: L 104 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7425 (ttpp) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.3194 time to fit residues: 25.5379 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.179027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.173502 restraints weight = 2767.478| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 0.67 r_work: 0.3822 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 2881 Z= 0.317 Angle : 0.721 7.290 3929 Z= 0.364 Chirality : 0.049 0.159 450 Planarity : 0.006 0.047 481 Dihedral : 5.556 18.070 384 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.36 % Allowed : 14.64 % Favored : 80.00 % 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: 0.06 (0.45), residues: 334 helix: None (None), residues: 0 sheet: 0.03 (0.40), residues: 144 loop : 0.19 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.011 0.002 TYR H 59 PHE 0.016 0.002 PHE A 133 TRP 0.005 0.001 TRP H 52 HIS 0.005 0.002 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.32 ( 2872) covalent geometry : angle 0.69456 / 0.36 ( 3905) SS BOND : bond 0.00140 / 0.07 ( 3) SS BOND : angle 3.62323 / 2.04 ( 6) hydrogen bonds : bond 0.04046 / 2.76 ( 94) hydrogen bonds : angle 6.52346 / 4.42 ( 225) link_ALPHA1-4 : bond 0.01757 / 0.92 ( 1) link_ALPHA1-4 : angle 2.05548 / 0.99 ( 3) link_BETA1-4 : bond 0.00442 / 0.23 ( 1) link_BETA1-4 : angle 1.53741 / 0.78 ( 3) link_BETA1-6 : bond 0.00243 / 0.13 ( 1) link_BETA1-6 : angle 1.11415 / 0.59 ( 3) link_NAG-ASN : bond 0.00109 / 0.05 ( 3) link_NAG-ASN : angle 2.51063 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.067 Fit side-chains REVERT: A 190 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6925 (mtt-85) REVERT: A 248 TYR cc_start: 0.8406 (t80) cc_final: 0.8141 (t80) REVERT: H 45 LEU cc_start: 0.8771 (mt) cc_final: 0.8567 (mt) REVERT: H 80 TYR cc_start: 0.7324 (m-80) cc_final: 0.6853 (m-80) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.3283 time to fit residues: 31.2199 Evaluate side-chains 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 11 optimal weight: 0.0870 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 overall best weight: 0.0914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.182216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.176801 restraints weight = 2799.403| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 0.68 r_work: 0.3841 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2881 Z= 0.111 Angle : 0.540 4.592 3929 Z= 0.279 Chirality : 0.044 0.165 450 Planarity : 0.004 0.040 481 Dihedral : 4.650 15.322 384 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.64 % Allowed : 17.14 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.37 (0.41), residues: 149 loop : 0.38 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.010 0.001 TYR L 86 PHE 0.009 0.001 PHE A 133 TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 2872) covalent geometry : angle 0.52537 / 0.27 ( 3905) SS BOND : bond 0.00126 / 0.06 ( 3) SS BOND : angle 1.94388 / 1.13 ( 6) hydrogen bonds : bond 0.03033 / 2.11 ( 94) hydrogen bonds : angle 6.04331 / 4.06 ( 225) link_ALPHA1-4 : bond 0.01528 / 0.80 ( 1) link_ALPHA1-4 : angle 2.16307 / 1.03 ( 3) link_BETA1-4 : bond 0.00510 / 0.27 ( 1) link_BETA1-4 : angle 1.34106 / 0.63 ( 3) link_BETA1-6 : bond 0.00198 / 0.10 ( 1) link_BETA1-6 : angle 1.07410 / 0.55 ( 3) link_NAG-ASN : bond 0.00279 / 0.14 ( 3) link_NAG-ASN : angle 1.51173 / 0.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.060 Fit side-chains REVERT: A 248 TYR cc_start: 0.8266 (t80) cc_final: 0.8024 (t80) REVERT: L 9 SER cc_start: 0.5427 (p) cc_final: 0.4960 (t) REVERT: L 104 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7610 (ttpp) REVERT: H 27 PHE cc_start: 0.7549 (p90) cc_final: 0.7344 (p90) REVERT: H 38 ARG cc_start: 0.8633 (ptt180) cc_final: 0.8322 (ptt180) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.3234 time to fit residues: 26.1068 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.177456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.172016 restraints weight = 2781.445| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 0.65 r_work: 0.3809 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 2881 Z= 0.364 Angle : 0.779 7.830 3929 Z= 0.389 Chirality : 0.052 0.182 450 Planarity : 0.006 0.046 481 Dihedral : 5.910 19.355 384 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.29 % Allowed : 17.86 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.45), residues: 334 helix: None (None), residues: 0 sheet: -0.15 (0.40), residues: 144 loop : -0.03 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 36 TYR 0.014 0.002 TYR L 33 PHE 0.019 0.002 PHE A 133 TRP 0.006 0.002 TRP H 52 HIS 0.006 0.002 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.36 ( 2872) covalent geometry : angle 0.75509 / 0.38 ( 3905) SS BOND : bond 0.00282 / 0.14 ( 3) SS BOND : angle 3.57163 / 2.00 ( 6) hydrogen bonds : bond 0.04195 / 2.87 ( 94) hydrogen bonds : angle 6.69394 / 4.49 ( 225) link_ALPHA1-4 : bond 0.01755 / 0.92 ( 1) link_ALPHA1-4 : angle 1.81395 / 0.87 ( 3) link_BETA1-4 : bond 0.00477 / 0.25 ( 1) link_BETA1-4 : angle 1.65026 / 0.85 ( 3) link_BETA1-6 : bond 0.00150 / 0.08 ( 1) link_BETA1-6 : angle 1.08969 / 0.59 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 3) link_NAG-ASN : angle 2.58773 / 1.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.075 Fit side-chains REVERT: A 248 TYR cc_start: 0.8403 (t80) cc_final: 0.8154 (t80) REVERT: H 80 TYR cc_start: 0.7345 (m-80) cc_final: 0.6861 (m-80) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.2484 time to fit residues: 21.6072 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 chunk 13 optimal weight: 0.0570 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 0.0870 chunk 23 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.178274 restraints weight = 2849.510| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 0.68 r_work: 0.3875 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2881 Z= 0.115 Angle : 0.571 5.480 3929 Z= 0.296 Chirality : 0.045 0.168 450 Planarity : 0.004 0.039 481 Dihedral : 4.746 16.233 384 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.29 % Allowed : 18.93 % Favored : 76.79 % 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: 0.21 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.02 (0.39), residues: 155 loop : 0.43 (0.51), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.011 0.001 TYR L 86 PHE 0.009 0.001 PHE A 133 TRP 0.006 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 2872) covalent geometry : angle 0.55011 / 0.29 ( 3905) SS BOND : bond 0.00244 / 0.12 ( 3) SS BOND : angle 3.08410 / 1.77 ( 6) hydrogen bonds : bond 0.03061 / 2.16 ( 94) hydrogen bonds : angle 6.12836 / 4.10 ( 225) link_ALPHA1-4 : bond 0.01459 / 0.77 ( 1) link_ALPHA1-4 : angle 2.03835 / 0.96 ( 3) link_BETA1-4 : bond 0.00621 / 0.33 ( 1) link_BETA1-4 : angle 1.35152 / 0.63 ( 3) link_BETA1-6 : bond 0.00205 / 0.11 ( 1) link_BETA1-6 : angle 1.09305 / 0.56 ( 3) link_NAG-ASN : bond 0.00257 / 0.13 ( 3) link_NAG-ASN : angle 1.46911 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.099 Fit side-chains REVERT: A 191 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5390 (tp30) REVERT: A 248 TYR cc_start: 0.8296 (t80) cc_final: 0.8089 (t80) REVERT: L 9 SER cc_start: 0.5481 (p) cc_final: 0.5001 (t) REVERT: H 27 PHE cc_start: 0.7587 (p90) cc_final: 0.7376 (p90) REVERT: H 80 TYR cc_start: 0.7216 (m-80) cc_final: 0.6805 (m-80) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 0.3327 time to fit residues: 27.3254 Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 24 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.180818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.175187 restraints weight = 2836.978| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 0.70 r_work: 0.3840 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2881 Z= 0.216 Angle : 0.651 6.488 3929 Z= 0.328 Chirality : 0.047 0.170 450 Planarity : 0.005 0.043 481 Dihedral : 5.219 16.852 384 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.57 % Allowed : 20.00 % Favored : 76.43 % 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: -0.12 (0.46), residues: 334 helix: None (None), residues: 0 sheet: -0.16 (0.41), residues: 147 loop : 0.13 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.012 0.002 TYR L 33 PHE 0.014 0.002 PHE A 133 TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 2872) covalent geometry : angle 0.63014 / 0.32 ( 3905) SS BOND : bond 0.00268 / 0.13 ( 3) SS BOND : angle 3.31345 / 1.90 ( 6) hydrogen bonds : bond 0.03445 / 2.40 ( 94) hydrogen bonds : angle 6.32871 / 4.26 ( 225) link_ALPHA1-4 : bond 0.01584 / 0.83 ( 1) link_ALPHA1-4 : angle 1.81771 / 0.85 ( 3) link_BETA1-4 : bond 0.00566 / 0.30 ( 1) link_BETA1-4 : angle 1.50607 / 0.76 ( 3) link_BETA1-6 : bond 0.00214 / 0.11 ( 1) link_BETA1-6 : angle 1.07157 / 0.56 ( 3) link_NAG-ASN : bond 0.00109 / 0.05 ( 3) link_NAG-ASN : angle 1.84004 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.105 Fit side-chains REVERT: A 248 TYR cc_start: 0.8381 (t80) cc_final: 0.8138 (t80) REVERT: L 31 TYR cc_start: 0.8492 (m-10) cc_final: 0.8284 (m-10) REVERT: H 80 TYR cc_start: 0.7261 (m-80) cc_final: 0.6857 (m-80) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.3679 time to fit residues: 28.9272 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.0870 chunk 25 optimal weight: 0.0670 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.181955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.176261 restraints weight = 2842.908| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.70 r_work: 0.3855 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2881 Z= 0.173 Angle : 0.625 6.255 3929 Z= 0.319 Chirality : 0.047 0.176 450 Planarity : 0.004 0.041 481 Dihedral : 5.093 16.909 384 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.86 % Allowed : 21.07 % Favored : 76.07 % 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: -0.10 (0.47), residues: 334 helix: None (None), residues: 0 sheet: -0.15 (0.41), residues: 148 loop : 0.15 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.013 0.002 TYR L 33 PHE 0.019 0.001 PHE H 27 TRP 0.006 0.001 TRP A 152 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 2872) covalent geometry : angle 0.60487 / 0.31 ( 3905) SS BOND : bond 0.00298 / 0.15 ( 3) SS BOND : angle 3.15627 / 1.82 ( 6) hydrogen bonds : bond 0.03308 / 2.32 ( 94) hydrogen bonds : angle 6.28031 / 4.22 ( 225) link_ALPHA1-4 : bond 0.01497 / 0.79 ( 1) link_ALPHA1-4 : angle 1.81249 / 0.85 ( 3) link_BETA1-4 : bond 0.00566 / 0.30 ( 1) link_BETA1-4 : angle 1.47642 / 0.72 ( 3) link_BETA1-6 : bond 0.00210 / 0.11 ( 1) link_BETA1-6 : angle 1.07746 / 0.56 ( 3) link_NAG-ASN : bond 0.00159 / 0.08 ( 3) link_NAG-ASN : angle 1.68694 / 0.93 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.104 Fit side-chains REVERT: A 248 TYR cc_start: 0.8373 (t80) cc_final: 0.8127 (t80) REVERT: L 31 TYR cc_start: 0.8453 (m-10) cc_final: 0.8209 (m-10) REVERT: H 80 TYR cc_start: 0.7239 (m-80) cc_final: 0.6867 (m-80) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.3339 time to fit residues: 25.9747 Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.183182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.177276 restraints weight = 2925.533| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 0.77 r_work: 0.3865 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 2881 Z= 0.271 Angle : 0.712 7.256 3929 Z= 0.358 Chirality : 0.050 0.193 450 Planarity : 0.005 0.044 481 Dihedral : 5.558 17.972 384 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.21 % Allowed : 20.71 % Favored : 76.07 % 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: -0.24 (0.46), residues: 334 helix: None (None), residues: 0 sheet: -0.12 (0.42), residues: 135 loop : -0.08 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.014 0.002 TYR L 33 PHE 0.016 0.002 PHE H 27 TRP 0.005 0.001 TRP H 52 HIS 0.007 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 ( 2872) covalent geometry : angle 0.68997 / 0.35 ( 3905) SS BOND : bond 0.00297 / 0.15 ( 3) SS BOND : angle 3.38977 / 1.94 ( 6) hydrogen bonds : bond 0.03768 / 2.63 ( 94) hydrogen bonds : angle 6.53148 / 4.39 ( 225) link_ALPHA1-4 : bond 0.01544 / 0.81 ( 1) link_ALPHA1-4 : angle 1.69271 / 0.79 ( 3) link_BETA1-4 : bond 0.00632 / 0.33 ( 1) link_BETA1-4 : angle 1.69253 / 0.86 ( 3) link_BETA1-6 : bond 0.00234 / 0.12 ( 1) link_BETA1-6 : angle 1.02538 / 0.55 ( 3) link_NAG-ASN : bond 0.00097 / 0.05 ( 3) link_NAG-ASN : angle 2.14316 / 1.16 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.17 seconds wall clock time: 22 minutes 35.20 seconds (1355.20 seconds total)