Starting phenix.real_space_refine on Sat Dec 9 19:50:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/12_2023/8e55_27903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/12_2023/8e55_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_27903/12_2023/8e55_27903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/12_2023/8e55_27903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/12_2023/8e55_27903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e55_27903/12_2023/8e55_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-1.21rc1-5172/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: 5.64, 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: 11.00 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: 0.77 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: 4.61 Time building geometry restraints manager: 11.36 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: 4920 16.34 - 32.69: 336 32.69 - 49.03: 26 49.03 - 65.38: 11 65.38 - 81.72: 11 Dihedral angle restraints: 5304 sinusoidal: 2920 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 5301 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: 0.530 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: 0.200 Extract box with map and model: 3.010 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 44.510 Find NCS groups from input model: 0.530 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- 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 : 1.102 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: 0.5647 time to fit residues: 146.8641 Evaluate side-chains 138 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1382 time to fit residues: 2.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 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: 4.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.6370 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6092 Z= 0.263 Angle : 0.573 3.793 8164 Z= 0.317 Chirality : 0.030 0.117 1004 Planarity : 0.003 0.032 1044 Dihedral : 4.625 43.830 832 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.01 % Allowed : 11.41 % Favored : 87.58 % 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: 2.37 (0.29), residues: 764 helix: 1.65 (0.18), residues: 708 sheet: None (None), residues: 0 loop : 1.18 (0.96), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE A 181 TYR 0.011 0.002 TYR D 107 ARG 0.002 0.000 ARG A 190 *********************** 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 144 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.989 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 outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 0.3833 time to fit residues: 72.7772 Evaluate side-chains 130 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1642 time to fit residues: 2.2346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 61 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- 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: 0.6312 moved from start: 0.4470 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= 0.181 Angle : 0.529 5.109 8164 Z= 0.284 Chirality : 0.030 0.110 1004 Planarity : 0.003 0.033 1044 Dihedral : 3.969 29.634 832 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.51 % Allowed : 11.91 % Favored : 86.58 % 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: 3.03 (0.30), residues: 764 helix: 2.08 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.34 (1.01), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 181 TYR 0.004 0.001 TYR D 107 ARG 0.002 0.000 ARG D 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 144 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.038 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 outliers start: 9 outliers final: 8 residues processed: 143 average time/residue: 0.3649 time to fit residues: 69.5683 Evaluate side-chains 134 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.110 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1405 time to fit residues: 3.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.6372 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6092 Z= 0.239 Angle : 0.542 4.658 8164 Z= 0.292 Chirality : 0.029 0.112 1004 Planarity : 0.003 0.035 1044 Dihedral : 3.747 21.119 832 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.84 % Allowed : 14.09 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.01 (0.30), residues: 764 helix: 2.08 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.19 (1.02), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.008 0.001 TYR D 107 ARG 0.003 0.000 ARG A 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 136 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.992 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 outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 0.3637 time to fit residues: 65.0978 Evaluate side-chains 128 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1430 time to fit residues: 2.4285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 1 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.6331 moved from start: 0.5042 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= 0.182 Angle : 0.508 4.528 8164 Z= 0.270 Chirality : 0.029 0.103 1004 Planarity : 0.003 0.034 1044 Dihedral : 3.511 17.497 832 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.67 % Allowed : 14.26 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.44 (0.30), residues: 764 helix: 2.37 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.15 (1.03), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 181 TYR 0.008 0.001 TYR D 107 ARG 0.002 0.000 ARG B 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 144 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.154 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 outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 0.4105 time to fit residues: 78.2073 Evaluate side-chains 124 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1470 time to fit residues: 1.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.6415 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6092 Z= 0.278 Angle : 0.571 4.945 8164 Z= 0.306 Chirality : 0.030 0.155 1004 Planarity : 0.004 0.034 1044 Dihedral : 3.606 19.071 832 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.67 % Allowed : 17.28 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.30), residues: 764 helix: 2.17 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.21 (1.03), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 181 TYR 0.007 0.001 TYR D 107 ARG 0.003 0.000 ARG D 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 122 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.140 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: 4 outliers final: 2 residues processed: 122 average time/residue: 0.3559 time to fit residues: 58.9597 Evaluate side-chains 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1432 time to fit residues: 1.8472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.6340 moved from start: 0.5478 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= 0.173 Angle : 0.499 4.519 8164 Z= 0.265 Chirality : 0.029 0.121 1004 Planarity : 0.003 0.034 1044 Dihedral : 3.388 16.097 832 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.34 % Allowed : 17.28 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.30), residues: 764 helix: 2.55 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.26 (1.06), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 165 TYR 0.008 0.001 TYR D 107 ARG 0.002 0.000 ARG D 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 129 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.079 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 outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.3540 time to fit residues: 61.5903 Evaluate side-chains 119 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.6437 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6092 Z= 0.286 Angle : 0.578 4.314 8164 Z= 0.310 Chirality : 0.030 0.106 1004 Planarity : 0.004 0.033 1044 Dihedral : 3.521 17.569 832 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 17.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.30), residues: 764 helix: 2.27 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.30 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 181 TYR 0.009 0.001 TYR D 107 ARG 0.004 0.000 ARG D 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 127 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.123 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 outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.3588 time to fit residues: 61.2961 Evaluate side-chains 123 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1514 time to fit residues: 1.9878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6345 moved from start: 0.5703 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= 0.164 Angle : 0.502 4.463 8164 Z= 0.265 Chirality : 0.029 0.105 1004 Planarity : 0.003 0.034 1044 Dihedral : 3.342 15.530 832 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.17 % Allowed : 18.29 % Favored : 81.54 % 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: 3.92 (0.30), residues: 764 helix: 2.68 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.29 (1.05), 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 0.002 0.000 ARG D 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 124 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.988 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 outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.3403 time to fit residues: 57.0654 Evaluate side-chains 116 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1346 time to fit residues: 1.5377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.6323 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6092 Z= 0.155 Angle : 0.505 4.734 8164 Z= 0.266 Chirality : 0.029 0.146 1004 Planarity : 0.003 0.034 1044 Dihedral : 3.209 16.551 832 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 18.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.12 (0.30), residues: 764 helix: 2.81 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.28 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE A 181 TYR 0.003 0.001 TYR C 107 ARG 0.002 0.000 ARG D 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 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.141 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 outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3467 time to fit residues: 56.4707 Evaluate side-chains 116 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.189218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160457 restraints weight = 31625.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.169178 restraints weight = 17646.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.174869 restraints weight = 11477.947| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6092 Z= 0.206 Angle : 0.528 4.665 8164 Z= 0.280 Chirality : 0.029 0.115 1004 Planarity : 0.003 0.033 1044 Dihedral : 3.214 16.753 832 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 18.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.14 (0.30), residues: 764 helix: 2.82 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.29 (1.03), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 181 TYR 0.004 0.001 TYR A 107 ARG 0.002 0.000 ARG B 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.78 seconds wall clock time: 50 minutes 47.55 seconds (3047.55 seconds total)