Starting phenix.real_space_refine on Tue Jul 29 20:52:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.map" model { file = "/net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e55_27903/07_2025/8e55_27903.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 3892 2.51 5 N 1040 2.21 5 O 1132 1.98 5 H 6104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3044 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3044 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3044 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3044 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 5.86, per 1000 atoms: 0.48 Number of scatterers: 12176 At special positions: 0 Unit cell: (94.92, 94.92, 53.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 1132 8.00 N 1040 7.00 C 3892 6.00 H 6104 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 97.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 57 removed outlier: 4.003A pdb=" N GLU A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 82 removed outlier: 3.547A pdb=" N GLU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 117 removed outlier: 3.983A pdb=" N GLU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 142 Processing helix chain 'A' and resid 144 through 172 removed outlier: 4.322A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 3.979A pdb=" N ARG A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 57 removed outlier: 3.968A pdb=" N GLU B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 82 Processing helix chain 'B' and resid 84 through 117 removed outlier: 4.043A pdb=" N GLU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 142 Processing helix chain 'B' and resid 144 through 172 removed outlier: 4.222A pdb=" N GLU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 202 removed outlier: 3.723A pdb=" N ARG B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 57 removed outlier: 3.960A pdb=" N GLU C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 82 removed outlier: 3.607A pdb=" N GLU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 117 removed outlier: 3.956A pdb=" N GLU C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 142 Processing helix chain 'C' and resid 144 through 172 removed outlier: 4.156A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 202 removed outlier: 3.710A pdb=" N ARG C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 26 through 57 removed outlier: 3.950A pdb=" N GLU D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 82 Processing helix chain 'D' and resid 84 through 117 removed outlier: 3.947A pdb=" N GLU D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 142 Processing helix chain 'D' and resid 144 through 172 removed outlier: 4.247A pdb=" N GLU D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 202 removed outlier: 4.045A pdb=" N ARG D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1737 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: 4.35 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6104 1.03 - 1.22: 0 1.22 - 1.41: 2212 1.41 - 1.60: 3864 1.60 - 1.79: 16 Bond restraints: 12196 Sorted by residual: bond pdb=" CB LYS B 158 " pdb=" CG LYS B 158 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CB LYS C 158 " pdb=" CG LYS C 158 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB LYS D 158 " pdb=" CG LYS D 158 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB ILE D 157 " pdb=" CG2 ILE D 157 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB LYS A 158 " pdb=" CG LYS A 158 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 12191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 20088 0.98 - 1.95: 1948 1.95 - 2.93: 120 2.93 - 3.91: 35 3.91 - 4.89: 13 Bond angle restraints: 22204 Sorted by residual: angle pdb=" N GLY A 22 " pdb=" CA GLY A 22 " pdb=" C GLY A 22 " ideal model delta sigma weight residual 111.16 116.05 -4.89 1.76e+00 3.23e-01 7.70e+00 angle pdb=" N GLY B 22 " pdb=" CA GLY B 22 " pdb=" C GLY B 22 " ideal model delta sigma weight residual 110.77 115.09 -4.32 1.59e+00 3.96e-01 7.37e+00 angle pdb=" C LYS A 21 " pdb=" N GLY A 22 " pdb=" CA GLY A 22 " ideal model delta sigma weight residual 122.16 120.09 2.07 7.70e-01 1.69e+00 7.26e+00 angle pdb=" N GLY C 22 " pdb=" CA GLY C 22 " pdb=" C GLY C 22 " ideal model delta sigma weight residual 110.77 114.96 -4.19 1.59e+00 3.96e-01 6.93e+00 angle pdb=" C ALA C 15 " pdb=" N ILE C 16 " pdb=" CA ILE C 16 " ideal model delta sigma weight residual 121.97 117.79 4.18 1.80e+00 3.09e-01 5.38e+00 ... (remaining 22199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 5060 16.34 - 32.69: 356 32.69 - 49.03: 38 49.03 - 65.38: 11 65.38 - 81.72: 11 Dihedral angle restraints: 5476 sinusoidal: 3092 harmonic: 2384 Sorted by residual: dihedral pdb=" CA ILE C 110 " pdb=" C ILE C 110 " pdb=" N LYS C 111 " pdb=" CA LYS C 111 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE D 110 " pdb=" C ILE D 110 " pdb=" N LYS D 111 " pdb=" CA LYS D 111 " ideal model delta harmonic sigma weight residual 180.00 164.40 15.60 0 5.00e+00 4.00e-02 9.73e+00 dihedral pdb=" CA LEU B 136 " pdb=" CB LEU B 136 " pdb=" CG LEU B 136 " pdb=" CD1 LEU B 136 " ideal model delta sinusoidal sigma weight residual 180.00 132.40 47.60 3 1.50e+01 4.44e-03 8.52e+00 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 626 0.021 - 0.042: 214 0.042 - 0.063: 99 0.063 - 0.084: 53 0.084 - 0.105: 12 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CA PRO D 144 " pdb=" N PRO D 144 " pdb=" C PRO D 144 " pdb=" CB PRO D 144 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.74e-01 chirality pdb=" CA PRO C 144 " pdb=" N PRO C 144 " pdb=" C PRO C 144 " pdb=" CB PRO C 144 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA PRO B 84 " pdb=" N PRO B 84 " pdb=" C PRO B 84 " pdb=" CB PRO B 84 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.51e-01 ... (remaining 1001 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 16 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE C 16 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE C 16 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU C 17 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 16 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ILE B 16 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE B 16 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU B 17 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 16 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ILE D 16 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE D 16 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU D 17 " 0.009 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 401 2.17 - 2.78: 25125 2.78 - 3.38: 33972 3.38 - 3.99: 39978 3.99 - 4.60: 67706 Nonbonded interactions: 167182 Sorted by model distance: nonbonded pdb=" O GLU B 45 " pdb="HD22 ASN B 49 " model vdw 1.562 2.450 nonbonded pdb=" O GLU A 45 " pdb="HD22 ASN A 49 " model vdw 1.575 2.450 nonbonded pdb=" O ASP C 83 " pdb=" H ALA C 86 " model vdw 1.587 2.450 nonbonded pdb=" O ASP D 83 " pdb=" H ALA D 86 " model vdw 1.587 2.450 nonbonded pdb=" O GLU D 45 " pdb="HD22 ASN D 49 " model vdw 1.605 2.450 ... (remaining 167177 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.790 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: 0.230 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 29.880 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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 : 0.007 0.046 6092 Z= 0.302 Angle : 0.670 4.885 8164 Z= 0.387 Chirality : 0.030 0.105 1004 Planarity : 0.004 0.029 1044 Dihedral : 12.357 81.721 2408 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.50 % Allowed : 1.01 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 764 helix: 0.93 (0.18), residues: 704 sheet: None (None), residues: 0 loop : 0.01 (0.94), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 181 TYR 0.013 0.003 TYR B 107 ARG 0.004 0.001 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.10257 ( 587) hydrogen bonds : angle 5.30255 ( 1737) covalent geometry : bond 0.00667 ( 6092) covalent geometry : angle 0.66958 ( 8164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 216 average time/residue: 0.5555 time to fit residues: 145.3651 Evaluate side-chains 138 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.188461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.161503 restraints weight = 32015.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.169965 restraints weight = 17657.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.175303 restraints weight = 11351.954| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6092 Z= 0.190 Angle : 0.590 4.233 8164 Z= 0.325 Chirality : 0.030 0.130 1004 Planarity : 0.004 0.035 1044 Dihedral : 4.796 36.222 838 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.17 % Allowed : 10.91 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.29), residues: 764 helix: 1.74 (0.18), residues: 708 sheet: None (None), residues: 0 loop : 0.74 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE D 181 TYR 0.012 0.002 TYR D 107 ARG 0.003 0.000 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 587) hydrogen bonds : angle 4.28584 ( 1737) covalent geometry : bond 0.00402 ( 6092) covalent geometry : angle 0.58973 ( 8164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9094 (mttt) cc_final: 0.8833 (mmmt) outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 0.3749 time to fit residues: 74.1862 Evaluate side-chains 136 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.187923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.161031 restraints weight = 32220.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.169682 restraints weight = 17324.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.175210 restraints weight = 11021.534| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6092 Z= 0.164 Angle : 0.567 4.796 8164 Z= 0.305 Chirality : 0.030 0.140 1004 Planarity : 0.003 0.039 1044 Dihedral : 4.425 36.846 838 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.85 % Allowed : 12.42 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.30), residues: 764 helix: 2.07 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.73 (1.06), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 181 TYR 0.007 0.001 TYR C 107 ARG 0.002 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 587) hydrogen bonds : angle 3.92842 ( 1737) covalent geometry : bond 0.00348 ( 6092) covalent geometry : angle 0.56655 ( 8164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8455 (mp) cc_final: 0.8174 (tt) REVERT: A 70 LYS cc_start: 0.9103 (mttt) cc_final: 0.8844 (mmmt) REVERT: A 88 GLU cc_start: 0.8299 (tp30) cc_final: 0.7909 (tm-30) REVERT: B 88 GLU cc_start: 0.8296 (tp30) cc_final: 0.7967 (tm-30) REVERT: D 29 ILE cc_start: 0.8465 (mp) cc_final: 0.8181 (tt) outliers start: 11 outliers final: 9 residues processed: 144 average time/residue: 0.4605 time to fit residues: 88.9461 Evaluate side-chains 134 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.185912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153585 restraints weight = 30016.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.164004 restraints weight = 15544.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.170726 restraints weight = 9684.591| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6092 Z= 0.160 Angle : 0.557 5.282 8164 Z= 0.299 Chirality : 0.030 0.139 1004 Planarity : 0.004 0.039 1044 Dihedral : 4.312 38.998 838 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.35 % Allowed : 12.42 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.30), residues: 764 helix: 2.19 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.66 (1.07), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 181 TYR 0.005 0.001 TYR C 107 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 587) hydrogen bonds : angle 3.79393 ( 1737) covalent geometry : bond 0.00345 ( 6092) covalent geometry : angle 0.55740 ( 8164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9155 (mttt) cc_final: 0.8853 (mmmt) REVERT: A 88 GLU cc_start: 0.8318 (tp30) cc_final: 0.7922 (tm-30) REVERT: B 88 GLU cc_start: 0.8367 (tp30) cc_final: 0.7984 (tm-30) outliers start: 14 outliers final: 13 residues processed: 140 average time/residue: 0.4897 time to fit residues: 92.7643 Evaluate side-chains 139 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.184573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.153682 restraints weight = 29946.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.163806 restraints weight = 15406.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.170393 restraints weight = 9509.294| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6092 Z= 0.149 Angle : 0.548 4.928 8164 Z= 0.291 Chirality : 0.030 0.152 1004 Planarity : 0.004 0.047 1044 Dihedral : 4.279 41.354 838 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.18 % Allowed : 12.25 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.30), residues: 764 helix: 2.34 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.72 (1.10), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 181 TYR 0.005 0.001 TYR C 107 ARG 0.008 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 587) hydrogen bonds : angle 3.64552 ( 1737) covalent geometry : bond 0.00321 ( 6092) covalent geometry : angle 0.54768 ( 8164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9123 (mttt) cc_final: 0.8865 (mmmt) REVERT: A 88 GLU cc_start: 0.8215 (tp30) cc_final: 0.7923 (tm-30) REVERT: B 88 GLU cc_start: 0.8239 (tp30) cc_final: 0.7948 (tm-30) REVERT: B 165 PHE cc_start: 0.7417 (m-80) cc_final: 0.7131 (m-10) outliers start: 13 outliers final: 11 residues processed: 148 average time/residue: 0.4401 time to fit residues: 86.7272 Evaluate side-chains 141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.184740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.152768 restraints weight = 29866.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.162746 restraints weight = 15692.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.169390 restraints weight = 9872.532| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6092 Z= 0.160 Angle : 0.558 4.909 8164 Z= 0.297 Chirality : 0.030 0.168 1004 Planarity : 0.004 0.052 1044 Dihedral : 4.340 43.325 838 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 15.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.30), residues: 764 helix: 2.39 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.74 (1.11), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 181 TYR 0.003 0.001 TYR A 107 ARG 0.008 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 587) hydrogen bonds : angle 3.64192 ( 1737) covalent geometry : bond 0.00348 ( 6092) covalent geometry : angle 0.55773 ( 8164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9073 (mttt) cc_final: 0.8826 (mmmt) REVERT: A 88 GLU cc_start: 0.8180 (tp30) cc_final: 0.7906 (tm-30) REVERT: B 88 GLU cc_start: 0.8267 (tp30) cc_final: 0.7962 (tm-30) REVERT: B 165 PHE cc_start: 0.7475 (m-80) cc_final: 0.7172 (m-10) REVERT: C 165 PHE cc_start: 0.7462 (m-80) cc_final: 0.7174 (m-10) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.4073 time to fit residues: 77.6109 Evaluate side-chains 134 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.184706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.152503 restraints weight = 29647.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.162369 restraints weight = 15786.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.168973 restraints weight = 9991.780| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6092 Z= 0.157 Angle : 0.555 5.126 8164 Z= 0.294 Chirality : 0.031 0.182 1004 Planarity : 0.004 0.049 1044 Dihedral : 4.368 44.821 838 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.18 % Allowed : 16.44 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.30), residues: 764 helix: 2.46 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.70 (1.09), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 181 TYR 0.003 0.001 TYR A 107 ARG 0.007 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 587) hydrogen bonds : angle 3.61199 ( 1737) covalent geometry : bond 0.00342 ( 6092) covalent geometry : angle 0.55527 ( 8164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9075 (mttt) cc_final: 0.8823 (mmmt) REVERT: A 88 GLU cc_start: 0.8172 (tp30) cc_final: 0.7895 (tm-30) REVERT: A 165 PHE cc_start: 0.7454 (m-80) cc_final: 0.7184 (m-10) REVERT: B 88 GLU cc_start: 0.8270 (tp30) cc_final: 0.7956 (tm-30) REVERT: B 165 PHE cc_start: 0.7477 (m-80) cc_final: 0.7162 (m-10) REVERT: C 165 PHE cc_start: 0.7432 (m-80) cc_final: 0.7135 (m-10) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.3966 time to fit residues: 73.3018 Evaluate side-chains 135 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.185116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.152872 restraints weight = 29929.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.162702 restraints weight = 16036.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.169287 restraints weight = 10148.959| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6092 Z= 0.149 Angle : 0.550 4.842 8164 Z= 0.291 Chirality : 0.031 0.167 1004 Planarity : 0.004 0.048 1044 Dihedral : 4.360 45.940 838 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 16.61 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.30), residues: 764 helix: 2.56 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.68 (1.08), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.003 0.001 TYR A 107 ARG 0.007 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 587) hydrogen bonds : angle 3.55926 ( 1737) covalent geometry : bond 0.00324 ( 6092) covalent geometry : angle 0.55008 ( 8164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9074 (mttt) cc_final: 0.8824 (mmmt) REVERT: A 88 GLU cc_start: 0.8138 (tp30) cc_final: 0.7851 (tm-30) REVERT: A 165 PHE cc_start: 0.7410 (m-80) cc_final: 0.7146 (m-10) REVERT: B 88 GLU cc_start: 0.8239 (tp30) cc_final: 0.7938 (tm-30) REVERT: B 165 PHE cc_start: 0.7468 (m-80) cc_final: 0.7145 (m-10) REVERT: C 165 PHE cc_start: 0.7418 (m-80) cc_final: 0.7123 (m-10) outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 0.4328 time to fit residues: 84.4179 Evaluate side-chains 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.181200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147228 restraints weight = 29508.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.157282 restraints weight = 15899.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.163851 restraints weight = 10213.607| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6092 Z= 0.261 Angle : 0.672 4.656 8164 Z= 0.359 Chirality : 0.033 0.166 1004 Planarity : 0.004 0.055 1044 Dihedral : 4.733 49.038 838 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 17.45 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.29), residues: 764 helix: 1.93 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.71 (1.04), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 181 TYR 0.013 0.002 TYR C 107 ARG 0.008 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 587) hydrogen bonds : angle 4.07949 ( 1737) covalent geometry : bond 0.00577 ( 6092) covalent geometry : angle 0.67167 ( 8164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9109 (mttt) cc_final: 0.8858 (mmmt) REVERT: A 88 GLU cc_start: 0.8335 (tp30) cc_final: 0.7976 (tm-30) REVERT: A 165 PHE cc_start: 0.7522 (m-80) cc_final: 0.7262 (m-10) REVERT: B 88 GLU cc_start: 0.8386 (tp30) cc_final: 0.8067 (tm-30) REVERT: B 165 PHE cc_start: 0.7496 (m-80) cc_final: 0.7170 (m-10) REVERT: C 165 PHE cc_start: 0.7527 (m-80) cc_final: 0.7214 (m-10) outliers start: 14 outliers final: 13 residues processed: 134 average time/residue: 0.4394 time to fit residues: 80.2384 Evaluate side-chains 134 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.183756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.151930 restraints weight = 29190.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.161340 restraints weight = 15974.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.167677 restraints weight = 10256.519| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6092 Z= 0.141 Angle : 0.564 4.395 8164 Z= 0.297 Chirality : 0.030 0.131 1004 Planarity : 0.004 0.048 1044 Dihedral : 4.571 49.034 838 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.34 % Allowed : 18.79 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.30), residues: 764 helix: 2.38 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.17 (1.05), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.005 0.001 TYR C 107 ARG 0.007 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 587) hydrogen bonds : angle 3.64261 ( 1737) covalent geometry : bond 0.00307 ( 6092) covalent geometry : angle 0.56402 ( 8164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9052 (mttt) cc_final: 0.8794 (mmmt) REVERT: A 88 GLU cc_start: 0.8146 (tp30) cc_final: 0.7844 (tm-30) REVERT: A 165 PHE cc_start: 0.7451 (m-80) cc_final: 0.7170 (m-10) REVERT: B 88 GLU cc_start: 0.8210 (tp30) cc_final: 0.7936 (tm-30) outliers start: 8 outliers final: 7 residues processed: 127 average time/residue: 0.3534 time to fit residues: 61.0027 Evaluate side-chains 123 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151981 restraints weight = 28965.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.162156 restraints weight = 15353.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.168923 restraints weight = 9753.636| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6092 Z= 0.138 Angle : 0.568 5.637 8164 Z= 0.298 Chirality : 0.030 0.156 1004 Planarity : 0.004 0.046 1044 Dihedral : 4.467 49.208 838 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.68 % Allowed : 17.95 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.30), residues: 764 helix: 2.51 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.09 (1.02), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 181 TYR 0.005 0.001 TYR C 107 ARG 0.007 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 587) hydrogen bonds : angle 3.57054 ( 1737) covalent geometry : bond 0.00303 ( 6092) covalent geometry : angle 0.56835 ( 8164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4051.68 seconds wall clock time: 73 minutes 31.98 seconds (4411.98 seconds total)