Starting phenix.real_space_refine on Fri Sep 11 00:01:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.cif Found real_map, /net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21gl_67656/09_2026/21gl_67656.map" } resolution = 3.25 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= 0.006 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 31 5.16 5 C 3535 2.51 5 N 951 2.21 5 O 1089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5606 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1389 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1353 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1477 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 183} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1373 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 181} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 2, 'PHE:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.24 Number of scatterers: 5606 At special positions: 0 Unit cell: (64.8, 104.76, 118.8, 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 31 16.00 O 1089 8.00 N 951 7.00 C 3535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 107 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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 A 301 " - " ASN A 125 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 245.4 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 42.6% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 162 through 225 Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.580A pdb=" N GLN B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 149 removed outlier: 3.608A pdb=" N GLU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 195 removed outlier: 3.579A pdb=" N ALA B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 216 removed outlier: 3.689A pdb=" N MET C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.546A pdb=" N LYS D 133 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 removed outlier: 3.904A pdb=" N ILE D 138 " --> pdb=" O ASN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 216 removed outlier: 4.217A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.515A pdb=" N GLU A 88 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 98 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.512A pdb=" N CYS A 49 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR C 39 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 37 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU A 53 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N ASP C 35 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU C 123 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 62 " --> pdb=" O GLY C 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 25 removed outlier: 7.038A pdb=" N ILE B 105 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.648A pdb=" N GLU B 35 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.804A pdb=" N PHE B 82 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 44 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 111 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 36 Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 44 removed outlier: 3.565A pdb=" N LEU D 44 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 85 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.550A pdb=" N ILE D 48 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP D 103 " --> pdb=" O ILE D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 343 hydrogen bonds defined for protein. 972 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: 0.79 Time building geometry restraints manager: 0.59 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: 1886 1.34 - 1.46: 918 1.46 - 1.58: 2842 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5700 Sorted by residual: bond pdb=" N GLU C 87 " pdb=" CA GLU C 87 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" C GLU C 87 " pdb=" O GLU C 87 " ideal model delta sigma weight residual 1.234 1.251 -0.017 1.19e-02 7.06e+03 1.96e+00 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C5 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 NAG A 301 " pdb=" O3 NAG A 301 " ideal model delta sigma weight residual 1.403 1.422 -0.019 2.00e-02 2.50e+03 9.42e-01 ... (remaining 5695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 7441 1.26 - 2.51: 212 2.51 - 3.77: 30 3.77 - 5.03: 4 5.03 - 6.28: 2 Bond angle restraints: 7689 Sorted by residual: angle pdb=" N ALA C 77 " pdb=" CA ALA C 77 " pdb=" C ALA C 77 " ideal model delta sigma weight residual 108.34 112.69 -4.35 1.31e+00 5.83e-01 1.10e+01 angle pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " pdb=" CG TYR A 39 " ideal model delta sigma weight residual 113.90 119.20 -5.30 1.80e+00 3.09e-01 8.67e+00 angle pdb=" CA GLU C 87 " pdb=" C GLU C 87 " pdb=" O GLU C 87 " ideal model delta sigma weight residual 121.19 118.51 2.68 1.10e+00 8.26e-01 5.95e+00 angle pdb=" CA ASP A 91 " pdb=" CB ASP A 91 " pdb=" CG ASP A 91 " ideal model delta sigma weight residual 112.60 114.98 -2.38 1.00e+00 1.00e+00 5.68e+00 angle pdb=" CA CYS C 47 " pdb=" CB CYS C 47 " pdb=" SG CYS C 47 " ideal model delta sigma weight residual 114.40 118.80 -4.40 2.30e+00 1.89e-01 3.67e+00 ... (remaining 7684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3106 17.84 - 35.67: 281 35.67 - 53.51: 46 53.51 - 71.35: 18 71.35 - 89.18: 6 Dihedral angle restraints: 3457 sinusoidal: 1377 harmonic: 2080 Sorted by residual: dihedral pdb=" CA CYS C 47 " pdb=" C CYS C 47 " pdb=" N PHE C 48 " pdb=" CA PHE C 48 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" SG CYS D 43 " pdb=" CB CYS D 108 " pdb=" SG CYS D 108 " pdb=" CA CYS D 108 " ideal model delta sinusoidal sigma weight residual 79.00 9.94 69.06 1 2.00e+01 2.50e-03 1.54e+01 dihedral pdb=" CA ILE D 48 " pdb=" C ILE D 48 " pdb=" N HIS D 49 " pdb=" CA HIS D 49 " ideal model delta harmonic sigma weight residual 180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 3454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 621 0.035 - 0.071: 177 0.071 - 0.106: 46 0.106 - 0.141: 19 0.141 - 0.176: 2 Chirality restraints: 865 Sorted by residual: chirality pdb=" CB ILE B 46 " pdb=" CA ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CG2 ILE B 46 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE D 117 " pdb=" N ILE D 117 " pdb=" C ILE D 117 " pdb=" CB ILE D 117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 862 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 91 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 92 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 117 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO D 118 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 118 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 118 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " -0.015 2.00e-02 2.50e+03 1.01e-02 2.06e+00 pdb=" CG TYR A 39 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " -0.002 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 962 2.77 - 3.30: 5340 3.30 - 3.84: 9160 3.84 - 4.37: 9935 4.37 - 4.90: 18526 Nonbonded interactions: 43923 Sorted by model distance: nonbonded pdb=" OE2 GLU A 147 " pdb=" OH TYR A 152 " model vdw 2.238 3.040 nonbonded pdb=" NH2 ARG B 159 " pdb=" OD1 ASN D 179 " model vdw 2.283 3.120 nonbonded pdb=" OE1 GLU B 31 " pdb=" NZ LYS D 42 " model vdw 2.299 3.120 nonbonded pdb=" OE1 GLN A 221 " pdb=" NE2 GLN C 213 " model vdw 2.314 3.120 nonbonded pdb=" NE2 GLN C 50 " pdb=" O PRO C 51 " model vdw 2.324 3.120 ... (remaining 43918 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: 6.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.003 0.029 5705 Z= 0.140 Angle : 0.501 6.283 7700 Z= 0.282 Chirality : 0.040 0.176 865 Planarity : 0.003 0.058 999 Dihedral : 14.823 89.182 2095 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.76 (0.35), residues: 704 helix: 3.85 (0.28), residues: 280 sheet: -1.58 (0.39), residues: 205 loop : -1.94 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 41 TYR 0.024 0.001 TYR A 39 PHE 0.013 0.002 PHE C 106 TRP 0.013 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5700) covalent geometry : angle 0.49997 / 0.28 ( 7689) SS BOND : bond 0.00375 / 0.19 ( 4) SS BOND : angle 1.00791 / 0.40 ( 8) hydrogen bonds : bond 0.16174 / 10.10 ( 341) hydrogen bonds : angle 6.31383 / 4.31 ( 972) link_NAG-ASN : bond 0.00124 / 0.07 ( 1) link_NAG-ASN : angle 1.40644 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 125 ASN cc_start: 0.8471 (t0) cc_final: 0.8065 (t0) REVERT: B 51 GLU cc_start: 0.8238 (pp20) cc_final: 0.7817 (pp20) REVERT: B 101 MET cc_start: 0.8160 (mmt) cc_final: 0.6654 (mmt) REVERT: C 109 ASP cc_start: 0.7699 (m-30) cc_final: 0.7492 (m-30) REVERT: D 168 MET cc_start: 0.8336 (tpt) cc_final: 0.8108 (tpt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0686 time to fit residues: 11.1716 Evaluate side-chains 101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS C 196 ASN C 202 ASN D 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145309 restraints weight = 6748.081| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.00 r_work: 0.3638 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5705 Z= 0.223 Angle : 0.607 7.930 7700 Z= 0.334 Chirality : 0.043 0.267 865 Planarity : 0.004 0.057 999 Dihedral : 5.662 51.910 784 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.57 % Allowed : 9.43 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.34), residues: 704 helix: 3.80 (0.27), residues: 281 sheet: -1.65 (0.39), residues: 190 loop : -2.09 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 194 TYR 0.032 0.002 TYR A 39 PHE 0.021 0.002 PHE B 92 TRP 0.013 0.001 TRP A 187 HIS 0.007 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 ( 5700) covalent geometry : angle 0.59912 / 0.33 ( 7689) SS BOND : bond 0.00554 / 0.27 ( 4) SS BOND : angle 2.88312 / 1.01 ( 8) hydrogen bonds : bond 0.04506 / 3.03 ( 341) hydrogen bonds : angle 4.68478 / 3.21 ( 972) link_NAG-ASN : bond 0.00063 / 0.03 ( 1) link_NAG-ASN : angle 1.59471 / 0.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8546 (t0) cc_final: 0.8200 (t0) REVERT: A 173 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 101 MET cc_start: 0.8269 (mmt) cc_final: 0.6944 (mmt) REVERT: C 52 MET cc_start: 0.8099 (tpt) cc_final: 0.7585 (tpt) REVERT: D 47 GLU cc_start: 0.7967 (pp20) cc_final: 0.7753 (pt0) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.0646 time to fit residues: 9.6585 Evaluate side-chains 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.184659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147116 restraints weight = 6703.240| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.99 r_work: 0.3665 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5705 Z= 0.163 Angle : 0.558 6.905 7700 Z= 0.307 Chirality : 0.041 0.203 865 Planarity : 0.004 0.051 999 Dihedral : 5.253 40.906 784 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.23 % Allowed : 13.38 % Favored : 84.39 % 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: 0.60 (0.34), residues: 704 helix: 3.75 (0.28), residues: 282 sheet: -1.67 (0.37), residues: 200 loop : -2.13 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.028 0.002 TYR A 39 PHE 0.017 0.002 PHE B 33 TRP 0.013 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 5700) covalent geometry : angle 0.54962 / 0.30 ( 7689) SS BOND : bond 0.00491 / 0.24 ( 4) SS BOND : angle 2.87378 / 1.07 ( 8) hydrogen bonds : bond 0.04089 / 2.74 ( 341) hydrogen bonds : angle 4.45385 / 3.05 ( 972) link_NAG-ASN : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : angle 1.85862 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8432 (t0) cc_final: 0.8098 (t0) REVERT: A 173 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 79 LYS cc_start: 0.8941 (tptm) cc_final: 0.8708 (tptm) REVERT: B 101 MET cc_start: 0.8332 (mmt) cc_final: 0.6880 (mmt) REVERT: C 52 MET cc_start: 0.8185 (tpt) cc_final: 0.7735 (tpt) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.0668 time to fit residues: 10.0183 Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.183539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145837 restraints weight = 6795.844| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.01 r_work: 0.3644 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5705 Z= 0.187 Angle : 0.572 7.275 7700 Z= 0.313 Chirality : 0.041 0.218 865 Planarity : 0.004 0.046 999 Dihedral : 5.045 42.044 784 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.57 % Allowed : 15.44 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.60 (0.34), residues: 704 helix: 3.74 (0.28), residues: 282 sheet: -1.63 (0.37), residues: 200 loop : -2.18 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.029 0.002 TYR A 39 PHE 0.014 0.002 PHE A 86 TRP 0.013 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 5700) covalent geometry : angle 0.56295 / 0.31 ( 7689) SS BOND : bond 0.00894 / 0.43 ( 4) SS BOND : angle 2.95337 / 1.12 ( 8) hydrogen bonds : bond 0.04067 / 2.74 ( 341) hydrogen bonds : angle 4.38211 / 3.00 ( 972) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 2.11359 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8392 (t0) cc_final: 0.8073 (t0) REVERT: B 101 MET cc_start: 0.8361 (mmt) cc_final: 0.6961 (mmt) REVERT: C 52 MET cc_start: 0.8312 (tpt) cc_final: 0.8050 (tpt) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.0683 time to fit residues: 10.1618 Evaluate side-chains 110 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145802 restraints weight = 6833.716| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.01 r_work: 0.3645 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5705 Z= 0.184 Angle : 0.562 7.137 7700 Z= 0.307 Chirality : 0.041 0.200 865 Planarity : 0.004 0.045 999 Dihedral : 5.003 42.135 784 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.74 % Allowed : 15.44 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.60 (0.34), residues: 704 helix: 3.77 (0.27), residues: 283 sheet: -1.61 (0.37), residues: 200 loop : -2.26 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 41 TYR 0.029 0.002 TYR A 39 PHE 0.014 0.002 PHE A 86 TRP 0.013 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 5700) covalent geometry : angle 0.54993 / 0.30 ( 7689) SS BOND : bond 0.00701 / 0.34 ( 4) SS BOND : angle 3.35664 / 1.24 ( 8) hydrogen bonds : bond 0.04026 / 2.71 ( 341) hydrogen bonds : angle 4.31464 / 2.96 ( 972) link_NAG-ASN : bond 0.00132 / 0.07 ( 1) link_NAG-ASN : angle 2.17395 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8414 (t0) cc_final: 0.8099 (t0) REVERT: B 101 MET cc_start: 0.8391 (mmt) cc_final: 0.6937 (mmt) REVERT: C 151 MET cc_start: 0.5767 (ptp) cc_final: 0.4489 (ptm) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.0661 time to fit residues: 9.8077 Evaluate side-chains 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.182780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145213 restraints weight = 6753.312| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.00 r_work: 0.3634 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5705 Z= 0.193 Angle : 0.583 7.467 7700 Z= 0.318 Chirality : 0.042 0.217 865 Planarity : 0.004 0.046 999 Dihedral : 5.062 42.511 784 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.43 % Allowed : 16.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.60 (0.34), residues: 704 helix: 3.77 (0.28), residues: 282 sheet: -1.61 (0.37), residues: 200 loop : -2.24 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.029 0.002 TYR A 39 PHE 0.014 0.002 PHE A 86 TRP 0.012 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 5700) covalent geometry : angle 0.57030 / 0.31 ( 7689) SS BOND : bond 0.00724 / 0.35 ( 4) SS BOND : angle 3.50333 / 1.31 ( 8) hydrogen bonds : bond 0.04030 / 2.72 ( 341) hydrogen bonds : angle 4.31464 / 2.95 ( 972) link_NAG-ASN : bond 0.00153 / 0.08 ( 1) link_NAG-ASN : angle 2.15453 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8425 (t0) cc_final: 0.8101 (t0) REVERT: B 101 MET cc_start: 0.8404 (mmt) cc_final: 0.6988 (mmt) REVERT: C 52 MET cc_start: 0.8228 (tpt) cc_final: 0.7871 (tpt) REVERT: D 148 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7533 (mm-30) outliers start: 20 outliers final: 16 residues processed: 109 average time/residue: 0.0646 time to fit residues: 9.6761 Evaluate side-chains 111 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 0.0000 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.187563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150163 restraints weight = 6808.404| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.10 r_work: 0.3690 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5705 Z= 0.120 Angle : 0.534 6.712 7700 Z= 0.289 Chirality : 0.040 0.194 865 Planarity : 0.003 0.045 999 Dihedral : 4.751 37.091 784 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.57 % Allowed : 17.50 % Favored : 79.93 % 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: 0.76 (0.33), residues: 704 helix: 3.93 (0.28), residues: 283 sheet: -1.67 (0.36), residues: 196 loop : -2.08 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.020 0.001 TYR A 39 PHE 0.011 0.001 PHE B 33 TRP 0.012 0.001 TRP A 187 HIS 0.003 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5700) covalent geometry : angle 0.52187 / 0.28 ( 7689) SS BOND : bond 0.00796 / 0.38 ( 4) SS BOND : angle 3.36045 / 1.33 ( 8) hydrogen bonds : bond 0.03567 / 2.40 ( 341) hydrogen bonds : angle 4.04652 / 2.77 ( 972) link_NAG-ASN : bond 0.00017 / 0.01 ( 1) link_NAG-ASN : angle 2.11816 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8328 (t0) cc_final: 0.8004 (t0) REVERT: B 51 GLU cc_start: 0.8274 (pp20) cc_final: 0.7852 (pp20) REVERT: B 101 MET cc_start: 0.8474 (mmt) cc_final: 0.6795 (mmt) REVERT: B 132 GLU cc_start: 0.7887 (mp0) cc_final: 0.7518 (mp0) REVERT: C 52 MET cc_start: 0.8093 (tpt) cc_final: 0.7633 (tpt) REVERT: D 41 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8269 (ttp80) REVERT: D 156 ASP cc_start: 0.7938 (m-30) cc_final: 0.7645 (m-30) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.0637 time to fit residues: 9.7138 Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142645 restraints weight = 6795.896| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.98 r_work: 0.3612 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.006 0.074 5705 Z= 0.268 Angle : 0.663 10.316 7700 Z= 0.358 Chirality : 0.045 0.257 865 Planarity : 0.004 0.048 999 Dihedral : 5.360 45.915 784 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.26 % Allowed : 17.50 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.55 (0.33), residues: 704 helix: 3.68 (0.27), residues: 282 sheet: -1.53 (0.37), residues: 196 loop : -2.31 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.034 0.002 TYR A 39 PHE 0.018 0.002 PHE A 86 TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.27 ( 5700) covalent geometry : angle 0.64843 / 0.35 ( 7689) SS BOND : bond 0.01155 / 0.55 ( 4) SS BOND : angle 4.22759 / 1.56 ( 8) hydrogen bonds : bond 0.04322 / 2.94 ( 341) hydrogen bonds : angle 4.40496 / 3.03 ( 972) link_NAG-ASN : bond 0.00285 / 0.15 ( 1) link_NAG-ASN : angle 2.09073 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8362 (pp20) cc_final: 0.7930 (pp20) REVERT: B 71 LYS cc_start: 0.8349 (mptt) cc_final: 0.8109 (mptt) REVERT: B 101 MET cc_start: 0.8386 (mmt) cc_final: 0.7083 (mmt) REVERT: B 132 GLU cc_start: 0.7912 (mp0) cc_final: 0.7193 (mp0) REVERT: B 136 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7296 (mp0) REVERT: C 206 MET cc_start: 0.7374 (mmm) cc_final: 0.7127 (mtp) outliers start: 19 outliers final: 15 residues processed: 105 average time/residue: 0.0693 time to fit residues: 9.8091 Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 202 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.190970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158025 restraints weight = 6469.020| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.39 r_work: 0.3699 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5705 Z= 0.144 Angle : 0.589 10.211 7700 Z= 0.315 Chirality : 0.042 0.226 865 Planarity : 0.004 0.047 999 Dihedral : 5.002 38.903 784 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.57 % Allowed : 18.52 % Favored : 78.90 % 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: 0.60 (0.33), residues: 704 helix: 3.77 (0.28), residues: 283 sheet: -1.72 (0.35), residues: 199 loop : -2.13 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.024 0.001 TYR A 39 PHE 0.011 0.001 PHE C 106 TRP 0.013 0.001 TRP A 187 HIS 0.003 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 5700) covalent geometry : angle 0.57549 / 0.31 ( 7689) SS BOND : bond 0.01189 / 0.57 ( 4) SS BOND : angle 3.77113 / 1.47 ( 8) hydrogen bonds : bond 0.03808 / 2.57 ( 341) hydrogen bonds : angle 4.12794 / 2.83 ( 972) link_NAG-ASN : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : angle 2.05588 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7545 (tt) REVERT: B 51 GLU cc_start: 0.8305 (pp20) cc_final: 0.7940 (pp20) REVERT: B 101 MET cc_start: 0.8408 (mmt) cc_final: 0.6881 (mmt) REVERT: B 132 GLU cc_start: 0.7958 (mp0) cc_final: 0.7623 (mp0) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.0644 time to fit residues: 9.2054 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 202 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158573 restraints weight = 6899.351| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.92 r_work: 0.3782 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5705 Z= 0.152 Angle : 0.607 9.845 7700 Z= 0.322 Chirality : 0.042 0.215 865 Planarity : 0.004 0.048 999 Dihedral : 5.036 39.786 784 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.57 % Allowed : 19.38 % Favored : 78.04 % 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: 0.62 (0.33), residues: 704 helix: 3.82 (0.28), residues: 283 sheet: -1.76 (0.35), residues: 200 loop : -2.12 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.025 0.002 TYR A 39 PHE 0.012 0.001 PHE A 86 TRP 0.012 0.001 TRP A 187 HIS 0.003 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5700) covalent geometry : angle 0.59453 / 0.32 ( 7689) SS BOND : bond 0.01100 / 0.52 ( 4) SS BOND : angle 3.69674 / 1.42 ( 8) hydrogen bonds : bond 0.03768 / 2.56 ( 341) hydrogen bonds : angle 4.08542 / 2.79 ( 972) link_NAG-ASN : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : angle 1.96826 / 1.14 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7461 (tt) REVERT: B 51 GLU cc_start: 0.8326 (pp20) cc_final: 0.7915 (pp20) REVERT: B 101 MET cc_start: 0.8455 (mmt) cc_final: 0.6897 (mmt) REVERT: B 132 GLU cc_start: 0.7842 (mp0) cc_final: 0.7540 (mp0) REVERT: D 41 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8222 (ttp80) outliers start: 15 outliers final: 14 residues processed: 99 average time/residue: 0.0656 time to fit residues: 8.8360 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.192434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.156400 restraints weight = 6866.484| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.91 r_work: 0.3738 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5705 Z= 0.189 Angle : 0.632 10.152 7700 Z= 0.333 Chirality : 0.043 0.218 865 Planarity : 0.004 0.049 999 Dihedral : 5.139 41.791 784 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.92 % Allowed : 18.70 % Favored : 78.39 % 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: 0.57 (0.33), residues: 704 helix: 3.76 (0.27), residues: 283 sheet: -1.77 (0.35), residues: 200 loop : -2.13 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.030 0.002 TYR A 39 PHE 0.014 0.002 PHE A 86 TRP 0.012 0.001 TRP A 187 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 5700) covalent geometry : angle 0.61963 / 0.33 ( 7689) SS BOND : bond 0.01084 / 0.52 ( 4) SS BOND : angle 3.73611 / 1.41 ( 8) hydrogen bonds : bond 0.03921 / 2.67 ( 341) hydrogen bonds : angle 4.15925 / 2.84 ( 972) link_NAG-ASN : bond 0.00138 / 0.07 ( 1) link_NAG-ASN : angle 1.95661 / 1.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.30 seconds wall clock time: 25 minutes 58.28 seconds (1558.28 seconds total)