Starting phenix.real_space_refine on Fri Jan 19 17:30:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_27903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_27903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_27903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_27903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/01_2024/8e55_27903.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.57, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 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: 11.20 Conformation dependent library (CDL) restraints added in 1.4 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: 1.01 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: 4.44 Time building geometry restraints manager: 11.46 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: 98.84 - 104.70: 32 104.70 - 110.56: 13609 110.56 - 116.42: 3131 116.42 - 122.27: 4218 122.27 - 128.13: 1214 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: 5052 16.34 - 32.69: 336 32.69 - 49.03: 26 49.03 - 65.38: 11 65.38 - 81.72: 11 Dihedral angle restraints: 5436 sinusoidal: 3052 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 5433 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 1.850 nonbonded pdb=" O GLU A 45 " pdb="HD22 ASN A 49 " model vdw 1.575 1.850 nonbonded pdb=" O ASP C 83 " pdb=" H ALA C 86 " model vdw 1.587 1.850 nonbonded pdb=" O ASP D 83 " pdb=" H ALA D 86 " model vdw 1.587 1.850 nonbonded pdb=" O GLU D 45 " pdb="HD22 ASN D 49 " model vdw 1.605 1.850 ... (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 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: 0.440 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: 0.180 Extract box with map and model: 2.990 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 44.240 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- 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= 0.426 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 1.085 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: 0.5601 time to fit residues: 146.3224 Evaluate side-chains 138 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.9980 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: 10.0000 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3721 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= 0.244 Angle : 0.566 3.917 8164 Z= 0.313 Chirality : 0.030 0.115 1004 Planarity : 0.003 0.032 1044 Dihedral : 5.067 45.381 838 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 10.40 % Favored : 88.09 % 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: 2.48 (0.29), residues: 764 helix: 1.72 (0.18), residues: 708 sheet: None (None), residues: 0 loop : 1.21 (0.96), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 181 TYR 0.011 0.002 TYR D 107 ARG 0.003 0.000 ARG C 25 *********************** 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 147 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.935 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 outliers start: 9 outliers final: 7 residues processed: 147 average time/residue: 0.3708 time to fit residues: 71.7955 Evaluate side-chains 135 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain D residue 45 GLU 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 38 optimal weight: 30.0000 chunk 21 optimal weight: 0.0870 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.4369 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= 0.213 Angle : 0.541 5.024 8164 Z= 0.293 Chirality : 0.030 0.111 1004 Planarity : 0.003 0.033 1044 Dihedral : 4.509 35.911 838 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.01 % Allowed : 12.08 % Favored : 85.91 % 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 (0.30), residues: 764 helix: 2.02 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.29 (0.99), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 181 TYR 0.007 0.001 TYR D 107 ARG 0.002 0.000 ARG C 130 *********************** 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 142 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.036 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 outliers start: 12 outliers final: 10 residues processed: 141 average time/residue: 0.3497 time to fit residues: 66.4145 Evaluate side-chains 135 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6092 Z= 0.225 Angle : 0.534 3.788 8164 Z= 0.290 Chirality : 0.030 0.141 1004 Planarity : 0.003 0.035 1044 Dihedral : 4.312 38.518 838 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % 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: 3.11 (0.30), residues: 764 helix: 2.14 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.16 (1.01), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.005 0.001 TYR D 107 ARG 0.002 0.000 ARG C 41 *********************** 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 144 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.013 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 outliers start: 12 outliers final: 10 residues processed: 141 average time/residue: 0.3413 time to fit residues: 65.1302 Evaluate side-chains 136 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 163 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.4935 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= 0.205 Angle : 0.539 6.175 8164 Z= 0.286 Chirality : 0.030 0.142 1004 Planarity : 0.003 0.049 1044 Dihedral : 4.220 40.639 838 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.68 % Allowed : 12.75 % Favored : 84.56 % 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: 3.36 (0.30), residues: 764 helix: 2.32 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.08 (1.02), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.002 0.001 TYR D 107 ARG 0.008 0.000 ARG C 41 *********************** 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 146 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.060 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: B 165 PHE cc_start: 0.6376 (m-80) cc_final: 0.6165 (m-10) outliers start: 16 outliers final: 11 residues processed: 144 average time/residue: 0.3465 time to fit residues: 67.3327 Evaluate side-chains 133 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 C residue 50 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE 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 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5122 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= 0.216 Angle : 0.542 5.393 8164 Z= 0.288 Chirality : 0.030 0.156 1004 Planarity : 0.004 0.052 1044 Dihedral : 4.197 41.507 838 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.52 % Allowed : 14.93 % Favored : 82.55 % 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: 3.40 (0.30), residues: 764 helix: 2.34 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.17 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 181 TYR 0.002 0.001 TYR A 107 ARG 0.008 0.000 ARG C 41 *********************** 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 145 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.105 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: B 165 PHE cc_start: 0.6526 (m-80) cc_final: 0.6280 (m-10) outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 0.3737 time to fit residues: 70.9428 Evaluate side-chains 130 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6092 Z= 0.214 Angle : 0.541 4.999 8164 Z= 0.289 Chirality : 0.030 0.152 1004 Planarity : 0.003 0.049 1044 Dihedral : 4.185 41.877 838 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.35 % Allowed : 16.28 % 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: 3.42 (0.30), residues: 764 helix: 2.34 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.25 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 165 TYR 0.003 0.001 TYR A 107 ARG 0.007 0.000 ARG C 41 *********************** 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 135 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.124 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 165 PHE cc_start: 0.6476 (m-80) cc_final: 0.6263 (m-10) REVERT: B 165 PHE cc_start: 0.6493 (m-80) cc_final: 0.6241 (m-10) outliers start: 14 outliers final: 5 residues processed: 134 average time/residue: 0.3551 time to fit residues: 65.5147 Evaluate side-chains 122 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 C residue 50 ILE Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6092 Z= 0.251 Angle : 0.565 5.379 8164 Z= 0.302 Chirality : 0.031 0.145 1004 Planarity : 0.004 0.051 1044 Dihedral : 4.261 42.599 838 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.18 % Allowed : 16.78 % 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: 3.30 (0.30), residues: 764 helix: 2.27 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.29 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 181 TYR 0.003 0.001 TYR A 107 ARG 0.008 0.000 ARG C 41 *********************** 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 135 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.069 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 165 PHE cc_start: 0.6571 (m-80) cc_final: 0.6304 (m-10) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 0.3378 time to fit residues: 61.6041 Evaluate side-chains 130 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 97 ILE 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 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6092 Z= 0.159 Angle : 0.506 4.925 8164 Z= 0.266 Chirality : 0.029 0.103 1004 Planarity : 0.003 0.044 1044 Dihedral : 4.092 42.114 838 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.68 % Allowed : 16.95 % 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: 3.93 (0.30), residues: 764 helix: 2.68 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.35 (1.05), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 181 TYR 0.002 0.000 TYR A 107 ARG 0.006 0.000 ARG C 41 *********************** 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 fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.072 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 165 PHE cc_start: 0.6571 (m-80) cc_final: 0.6312 (m-10) outliers start: 10 outliers final: 7 residues processed: 140 average time/residue: 0.3396 time to fit residues: 64.4607 Evaluate side-chains 127 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 C residue 50 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6092 Z= 0.188 Angle : 0.531 5.550 8164 Z= 0.280 Chirality : 0.030 0.108 1004 Planarity : 0.003 0.048 1044 Dihedral : 4.091 43.320 838 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.17 % Allowed : 17.95 % Favored : 80.87 % 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: 3.97 (0.30), residues: 764 helix: 2.71 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.37 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 181 TYR 0.008 0.001 TYR D 107 ARG 0.006 0.000 ARG C 41 ********************** 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 fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.971 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 outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.3891 time to fit residues: 66.7059 Evaluate side-chains 127 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 C residue 50 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 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 = 0.4483 r_free = 0.4483 target = 0.185603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.153192 restraints weight = 30905.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.163118 restraints weight = 16999.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.169421 restraints weight = 10914.682| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6092 Z= 0.218 Angle : 0.542 4.861 8164 Z= 0.288 Chirality : 0.030 0.129 1004 Planarity : 0.003 0.048 1044 Dihedral : 4.120 43.373 838 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.34 % Allowed : 17.95 % Favored : 80.70 % 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: 3.94 (0.30), residues: 764 helix: 2.68 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.38 (1.03), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 181 TYR 0.003 0.001 TYR A 107 ARG 0.007 0.000 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.44 seconds wall clock time: 50 minutes 36.06 seconds (3036.06 seconds total)