Starting phenix.real_space_refine on Wed Sep 17 22:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e55_27903/09_2025/8e55_27903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e55_27903/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e55_27903/09_2025/8e55_27903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e55_27903/09_2025/8e55_27903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e55_27903/09_2025/8e55_27903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e55_27903/09_2025/8e55_27903.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 2.19, per 1000 atoms: 0.18 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: 1.19 Conformation dependent library (CDL) restraints added in 324.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 2.66 Time building geometry restraints manager: 1.62 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: 0.00 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: 0.760 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 155 TYR 0.013 0.003 TYR B 107 PHE 0.010 0.001 PHE C 181 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 6092) covalent geometry : angle 0.66958 ( 8164) hydrogen bonds : bond 0.10257 ( 587) hydrogen bonds : angle 5.30255 ( 1737) *********************** 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 : 0.282 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 outliers start: 3 outliers final: 3 residues processed: 216 average time/residue: 0.2635 time to fit residues: 68.5809 Evaluate side-chains 134 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.186914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.159549 restraints weight = 32315.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.168140 restraints weight = 17806.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.173603 restraints weight = 11461.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.176969 restraints weight = 7922.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.179388 restraints weight = 5786.072| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6092 Z= 0.225 Angle : 0.631 4.569 8164 Z= 0.346 Chirality : 0.031 0.133 1004 Planarity : 0.004 0.035 1044 Dihedral : 4.797 35.276 838 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.34 % Allowed : 11.91 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.29), residues: 764 helix: 1.48 (0.18), residues: 708 sheet: None (None), residues: 0 loop : 0.66 (0.93), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 25 TYR 0.014 0.003 TYR D 107 PHE 0.012 0.001 PHE D 181 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 6092) covalent geometry : angle 0.63090 ( 8164) hydrogen bonds : bond 0.05035 ( 587) hydrogen bonds : angle 4.46990 ( 1737) *********************** 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 143 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.346 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: A 70 LYS cc_start: 0.9059 (mttt) cc_final: 0.8820 (mmmt) REVERT: A 88 GLU cc_start: 0.8203 (tp30) cc_final: 0.7919 (tm-30) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.1772 time to fit residues: 33.5091 Evaluate side-chains 132 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 46 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.187687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.160526 restraints weight = 32646.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.169388 restraints weight = 17676.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.174978 restraints weight = 11248.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178393 restraints weight = 7671.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.180871 restraints weight = 5515.066| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6092 Z= 0.162 Angle : 0.573 5.305 8164 Z= 0.306 Chirality : 0.031 0.152 1004 Planarity : 0.003 0.038 1044 Dihedral : 4.430 37.615 838 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 13.26 % Favored : 84.40 % 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 aren not related in a simple way. whole: 3.06 (0.30), residues: 764 helix: 2.01 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.64 (1.06), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.009 0.002 TYR C 107 PHE 0.008 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6092) covalent geometry : angle 0.57326 ( 8164) hydrogen bonds : bond 0.04552 ( 587) hydrogen bonds : angle 3.96356 ( 1737) *********************** 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 143 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.285 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: A 70 LYS cc_start: 0.9038 (mttt) cc_final: 0.8818 (mmmt) REVERT: A 88 GLU cc_start: 0.8166 (tp30) cc_final: 0.7884 (tm-30) REVERT: B 88 GLU cc_start: 0.8209 (tp30) cc_final: 0.7934 (tm-30) REVERT: D 29 ILE cc_start: 0.8392 (mp) cc_final: 0.8035 (tt) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.1715 time to fit residues: 32.1330 Evaluate side-chains 133 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 138 LEU 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 17 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.185529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.157888 restraints weight = 32068.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.166336 restraints weight = 17623.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.171875 restraints weight = 11394.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.175419 restraints weight = 7953.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.177931 restraints weight = 5820.806| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6092 Z= 0.212 Angle : 0.602 5.076 8164 Z= 0.323 Chirality : 0.031 0.152 1004 Planarity : 0.004 0.039 1044 Dihedral : 4.485 41.231 838 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.68 % Allowed : 14.26 % Favored : 83.05 % 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 aren not related in a simple way. whole: 2.94 (0.30), residues: 764 helix: 1.93 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.69 (1.06), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 41 TYR 0.011 0.002 TYR D 107 PHE 0.007 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6092) covalent geometry : angle 0.60166 ( 8164) hydrogen bonds : bond 0.04508 ( 587) hydrogen bonds : angle 4.04680 ( 1737) *********************** 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 139 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.358 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: A 88 GLU cc_start: 0.8127 (tp30) cc_final: 0.7893 (tm-30) REVERT: B 88 GLU cc_start: 0.8212 (tp30) cc_final: 0.7969 (tm-30) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.1742 time to fit residues: 31.8174 Evaluate side-chains 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain B residue 138 LEU 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 Chi-restraints excluded: chain D residue 127 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 3 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.187887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.160211 restraints weight = 32526.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.169307 restraints weight = 17497.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.174928 restraints weight = 11041.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.178419 restraints weight = 7531.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.180968 restraints weight = 5436.086| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5163 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= 0.140 Angle : 0.540 5.656 8164 Z= 0.286 Chirality : 0.030 0.143 1004 Planarity : 0.003 0.040 1044 Dihedral : 4.372 43.284 838 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 14.43 % Favored : 82.89 % 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 aren not related in a simple way. whole: 3.49 (0.30), residues: 764 helix: 2.31 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.61 (1.07), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.010 0.001 TYR D 107 PHE 0.006 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6092) covalent geometry : angle 0.54031 ( 8164) hydrogen bonds : bond 0.04118 ( 587) hydrogen bonds : angle 3.67849 ( 1737) *********************** 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 153 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.363 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: A 88 GLU cc_start: 0.8127 (tp30) cc_final: 0.7886 (tm-30) REVERT: B 88 GLU cc_start: 0.8196 (tp30) cc_final: 0.7930 (tm-30) REVERT: B 165 PHE cc_start: 0.7413 (m-80) cc_final: 0.7131 (m-10) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.1737 time to fit residues: 34.8691 Evaluate side-chains 142 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 B residue 97 ILE Chi-restraints excluded: chain B residue 138 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 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.189746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.162072 restraints weight = 32045.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.170865 restraints weight = 17331.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176471 restraints weight = 10988.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.180121 restraints weight = 7541.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.182743 restraints weight = 5392.087| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6092 Z= 0.120 Angle : 0.531 6.310 8164 Z= 0.277 Chirality : 0.030 0.126 1004 Planarity : 0.003 0.040 1044 Dihedral : 4.274 43.686 838 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.85 % Allowed : 16.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (0.30), residues: 764 helix: 2.61 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 2.69 (1.10), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 31 TYR 0.009 0.002 TYR C 107 PHE 0.006 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6092) covalent geometry : angle 0.53118 ( 8164) hydrogen bonds : bond 0.03821 ( 587) hydrogen bonds : angle 3.42692 ( 1737) *********************** 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 153 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.282 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: B 88 GLU cc_start: 0.8187 (tp30) cc_final: 0.7908 (tm-30) REVERT: B 165 PHE cc_start: 0.7441 (m-80) cc_final: 0.7119 (m-10) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.1756 time to fit residues: 34.3981 Evaluate side-chains 137 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.186946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.158325 restraints weight = 32023.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.167127 restraints weight = 17763.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.172668 restraints weight = 11489.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.176268 restraints weight = 8039.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.178839 restraints weight = 5898.314| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6092 Z= 0.176 Angle : 0.591 5.205 8164 Z= 0.313 Chirality : 0.033 0.193 1004 Planarity : 0.004 0.039 1044 Dihedral : 4.352 45.396 838 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.02 % Allowed : 17.79 % Favored : 79.19 % 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 aren not related in a simple way. whole: 3.51 (0.30), residues: 764 helix: 2.40 (0.18), residues: 708 sheet: None (None), residues: 0 loop : 1.25 (1.07), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 130 TYR 0.010 0.002 TYR C 107 PHE 0.005 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6092) covalent geometry : angle 0.59082 ( 8164) hydrogen bonds : bond 0.03990 ( 587) hydrogen bonds : angle 3.64970 ( 1737) *********************** 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 146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.259 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: A 165 PHE cc_start: 0.7384 (m-80) cc_final: 0.7142 (m-10) REVERT: B 45 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6985 (mm-30) REVERT: B 88 GLU cc_start: 0.8183 (tp30) cc_final: 0.7918 (tm-30) REVERT: B 165 PHE cc_start: 0.7471 (m-80) cc_final: 0.7144 (m-10) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.1755 time to fit residues: 33.0748 Evaluate side-chains 135 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 LEU 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 65 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.187440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.158747 restraints weight = 31993.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.167663 restraints weight = 17575.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.173248 restraints weight = 11322.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.176902 restraints weight = 7867.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.179314 restraints weight = 5725.770| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5760 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= 0.143 Angle : 0.557 4.540 8164 Z= 0.294 Chirality : 0.032 0.157 1004 Planarity : 0.003 0.039 1044 Dihedral : 4.334 45.916 838 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.35 % Allowed : 18.29 % Favored : 79.36 % 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 aren not related in a simple way. whole: 3.72 (0.30), residues: 764 helix: 2.55 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.24 (1.07), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 130 TYR 0.005 0.001 TYR D 107 PHE 0.005 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6092) covalent geometry : angle 0.55742 ( 8164) hydrogen bonds : bond 0.03876 ( 587) hydrogen bonds : angle 3.53979 ( 1737) *********************** 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 140 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.357 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: A 165 PHE cc_start: 0.7412 (m-80) cc_final: 0.7155 (m-10) REVERT: B 88 GLU cc_start: 0.8152 (tp30) cc_final: 0.7901 (tm-30) REVERT: B 165 PHE cc_start: 0.7471 (m-80) cc_final: 0.7148 (m-10) outliers start: 14 outliers final: 11 residues processed: 137 average time/residue: 0.1640 time to fit residues: 29.8938 Evaluate side-chains 136 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 138 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.0060 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.188309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160151 restraints weight = 31733.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.168861 restraints weight = 17417.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.174481 restraints weight = 11209.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.178105 restraints weight = 7719.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.180537 restraints weight = 5588.354| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6092 Z= 0.130 Angle : 0.542 4.696 8164 Z= 0.284 Chirality : 0.031 0.143 1004 Planarity : 0.003 0.039 1044 Dihedral : 4.282 46.150 838 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.01 % Allowed : 18.62 % Favored : 79.36 % 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 aren not related in a simple way. whole: 4.20 (0.30), residues: 764 helix: 2.78 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.71 (1.06), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 130 TYR 0.004 0.001 TYR D 107 PHE 0.004 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6092) covalent geometry : angle 0.54188 ( 8164) hydrogen bonds : bond 0.03767 ( 587) hydrogen bonds : angle 3.43203 ( 1737) *********************** 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 141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.363 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: A 165 PHE cc_start: 0.7416 (m-80) cc_final: 0.7146 (m-10) REVERT: B 88 GLU cc_start: 0.8179 (tp30) cc_final: 0.7922 (tm-30) REVERT: B 165 PHE cc_start: 0.7467 (m-80) cc_final: 0.7132 (m-10) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.1637 time to fit residues: 30.9304 Evaluate side-chains 132 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 B residue 97 ILE Chi-restraints excluded: chain B residue 138 LEU 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 54 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.188630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.160669 restraints weight = 31699.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.169393 restraints weight = 17350.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.174996 restraints weight = 11095.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.178496 restraints weight = 7652.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.181012 restraints weight = 5567.703| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6068 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= 0.123 Angle : 0.549 4.759 8164 Z= 0.286 Chirality : 0.031 0.139 1004 Planarity : 0.003 0.039 1044 Dihedral : 4.227 46.173 838 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.68 % Allowed : 19.63 % Favored : 78.69 % 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 aren not related in a simple way. whole: 4.30 (0.30), residues: 764 helix: 2.85 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.57 (1.04), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 130 TYR 0.003 0.001 TYR B 107 PHE 0.011 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6092) covalent geometry : angle 0.54913 ( 8164) hydrogen bonds : bond 0.03696 ( 587) hydrogen bonds : angle 3.37213 ( 1737) ********************** 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 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.279 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: A 165 PHE cc_start: 0.7413 (m-80) cc_final: 0.7135 (m-10) REVERT: B 88 GLU cc_start: 0.8141 (tp30) cc_final: 0.7912 (tm-30) outliers start: 10 outliers final: 9 residues processed: 130 average time/residue: 0.1484 time to fit residues: 26.4785 Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 B residue 97 ILE Chi-restraints excluded: chain B residue 138 LEU 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 5 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.186523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.157966 restraints weight = 31965.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.166523 restraints weight = 17701.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.172140 restraints weight = 11503.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.175668 restraints weight = 8041.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.178119 restraints weight = 5934.324| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6092 Z= 0.174 Angle : 0.585 4.729 8164 Z= 0.310 Chirality : 0.031 0.135 1004 Planarity : 0.004 0.039 1044 Dihedral : 4.293 47.065 838 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.85 % Allowed : 20.30 % Favored : 77.85 % 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 aren not related in a simple way. whole: 4.01 (0.29), residues: 764 helix: 2.68 (0.18), residues: 700 sheet: None (None), residues: 0 loop : 2.36 (1.04), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.005 0.001 TYR D 107 PHE 0.004 0.001 PHE A 181 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6092) covalent geometry : angle 0.58486 ( 8164) hydrogen bonds : bond 0.03892 ( 587) hydrogen bonds : angle 3.57670 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.28 seconds wall clock time: 33 minutes 14.71 seconds (1994.71 seconds total)