Starting phenix.real_space_refine on Wed Sep 17 02:57:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og3_20051/09_2025/6og3_20051.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 2 Type Number sf(0) Gaussians C 810 2.51 5 N 405 2.21 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1215 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 10, 'PHE:plan': 4, 'GLN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 210 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 10, 'PHE:plan': 4, 'GLN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 210 Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 10, 'PHE:plan': 4, 'GLN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 210 Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 27 Classifications: {'peptide': 9} Incomplete info: {'n_c_alpha_c_only': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 0.47, per 1000 atoms: 0.39 Number of scatterers: 1215 At special positions: 0 Unit cell: (54.696, 80.496, 75.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 2 Type Number sf(0) N 405 7.00 C 810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.05 Conformation dependent library (CDL) restraints added in 78.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'E' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 7 through 24' Processing helix chain 'E' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 30 through 40' Processing helix chain 'E' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 45 through 54' Processing helix chain 'E' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 56 through 69' Processing helix chain 'E' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 84 through 102' Processing helix chain 'E' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 107 through 117' Processing helix chain 'E' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 119 through 129' Processing helix chain 'E' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 132 through 142' Processing helix chain 'C' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 7 through 24' Processing helix chain 'C' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 30 through 40' Processing helix chain 'C' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 45 through 54' Processing helix chain 'C' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 56 through 69' Processing helix chain 'C' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 84 through 102' Processing helix chain 'C' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 107 through 117' Processing helix chain 'C' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 119 through 129' Processing helix chain 'C' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 132 through 142' Processing helix chain 'A' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 7 through 24' Processing helix chain 'A' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 30 through 40' Processing helix chain 'A' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 45 through 54' Processing helix chain 'A' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 56 through 69' Processing helix chain 'A' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 84 through 102' Processing helix chain 'A' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 107 through 117' Processing helix chain 'A' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 119 through 129' Processing helix chain 'A' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 132 through 142' No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.05 Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.37: 398 1.37 - 1.41: 0 1.41 - 1.45: 19 1.45 - 1.49: 386 1.49 - 1.54: 405 Bond restraints: 1208 Sorted by residual: bond pdb=" N ASP E 4 " pdb=" CA ASP E 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" N ASP C 4 " pdb=" CA ASP C 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 bond pdb=" N ASP A 4 " pdb=" CA ASP A 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.29e+00 bond pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 1.516 1.536 -0.020 1.72e-02 3.38e+03 1.33e+00 bond pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 1.456 1.471 -0.015 1.33e-02 5.65e+03 1.29e+00 ... (remaining 1203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 881 1.41 - 2.82: 245 2.82 - 4.22: 51 4.22 - 5.63: 15 5.63 - 7.04: 9 Bond angle restraints: 1201 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 110.42 117.09 -6.67 9.60e-01 1.09e+00 4.83e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 110.42 117.08 -6.66 9.60e-01 1.09e+00 4.82e+01 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 110.42 117.07 -6.65 9.60e-01 1.09e+00 4.81e+01 angle pdb=" N THR E 121 " pdb=" CA THR E 121 " pdb=" C THR E 121 " ideal model delta sigma weight residual 111.07 116.67 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 111.07 116.61 -5.54 1.07e+00 8.73e-01 2.68e+01 ... (remaining 1196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 0.84: 275 0.84 - 1.69: 96 1.69 - 2.53: 20 2.53 - 3.37: 3 3.37 - 4.22: 4 Dihedral angle restraints: 398 sinusoidal: 0 harmonic: 398 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 175.78 4.22 0 5.00e+00 4.00e-02 7.11e-01 dihedral pdb=" CA PHE E 28 " pdb=" C PHE E 28 " pdb=" N ILE E 29 " pdb=" CA ILE E 29 " ideal model delta harmonic sigma weight residual 180.00 176.36 3.64 0 5.00e+00 4.00e-02 5.31e-01 dihedral pdb=" CA PHE C 28 " pdb=" C PHE C 28 " pdb=" N ILE C 29 " pdb=" CA ILE C 29 " ideal model delta harmonic sigma weight residual 180.00 176.47 3.53 0 5.00e+00 4.00e-02 4.97e-01 ... (remaining 395 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.54 - 3.01: 471 3.01 - 3.48: 547 3.48 - 3.95: 768 3.95 - 4.43: 1587 4.43 - 4.90: 2121 Nonbonded interactions: 5494 Sorted by model distance: nonbonded pdb=" N ARG E 5 " pdb=" N LEU E 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG A 5 " pdb=" N LEU A 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG C 5 " pdb=" N LEU C 6 " model vdw 2.541 2.560 nonbonded pdb=" N ALA C 53 " pdb=" N GLY C 54 " model vdw 2.629 2.560 nonbonded pdb=" N ALA E 53 " pdb=" N GLY E 54 " model vdw 2.630 2.560 ... (remaining 5489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4858 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 : 0.005 0.031 1208 Z= 0.393 Angle : 1.530 7.041 1201 Z= 1.235 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 0.934 4.216 398 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 0.00 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.36), residues: 384 helix: 0.09 (0.24), residues: 318 sheet: None (None), residues: 0 loop : 1.54 (0.68), residues: 66 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 1208) covalent geometry : angle 1.52953 ( 1201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.029 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0070 time to fit residues: 0.0736 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 overall best weight: 3.2992 ------------------------------------------------------------------------------- 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 = 0.2686 r_free = 0.2686 target = 0.038652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.028041 restraints weight = 12411.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.028125 restraints weight = 11906.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.028161 restraints weight = 11531.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.028161 restraints weight = 11308.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.028161 restraints weight = 11308.993| |-----------------------------------------------------------------------------| r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.9282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1208 Z= 0.211 Angle : 0.546 2.464 1201 Z= 0.422 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.032 16.934 398 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.36), residues: 384 helix: 1.01 (0.32), residues: 209 sheet: None (None), residues: 0 loop : 0.81 (0.38), residues: 175 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 1208) covalent geometry : angle 0.54633 ( 1201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.086 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0037 time to fit residues: 0.0804 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 23 optimal weight: 0.0000 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 0.0060 overall best weight: 5.2006 ------------------------------------------------------------------------------- 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 = 0.2596 r_free = 0.2596 target = 0.035592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.026818 restraints weight = 12134.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.026624 restraints weight = 12783.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.026710 restraints weight = 12874.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2343 r_free = 0.2343 target = 0.026764 restraints weight = 11624.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.026834 restraints weight = 11456.995| |-----------------------------------------------------------------------------| r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 1.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1208 Z= 0.303 Angle : 0.675 2.833 1201 Z= 0.525 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.109 18.907 398 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.39), residues: 384 helix: 0.03 (0.36), residues: 196 sheet: None (None), residues: 0 loop : 0.69 (0.40), residues: 188 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 1208) covalent geometry : angle 0.67512 ( 1201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.031 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0037 time to fit residues: 0.0688 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 6.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.033274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2199 r_free = 0.2199 target = 0.023883 restraints weight = 14388.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2204 r_free = 0.2204 target = 0.023982 restraints weight = 13338.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2204 r_free = 0.2204 target = 0.023982 restraints weight = 12599.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2204 r_free = 0.2204 target = 0.023982 restraints weight = 12599.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2204 r_free = 0.2204 target = 0.023982 restraints weight = 12599.952| |-----------------------------------------------------------------------------| r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 1.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1208 Z= 0.336 Angle : 0.719 3.335 1201 Z= 0.564 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.365 19.771 398 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 34.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.41), residues: 384 helix: -0.70 (0.39), residues: 176 sheet: None (None), residues: 0 loop : 0.55 (0.41), residues: 208 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 1208) covalent geometry : angle 0.71869 ( 1201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.031 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0068 time to fit residues: 0.1022 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 0.0070 overall best weight: 1.6338 ------------------------------------------------------------------------------- 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 = 0.2584 r_free = 0.2584 target = 0.034597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025274 restraints weight = 11664.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025274 restraints weight = 12385.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025274 restraints weight = 12385.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025274 restraints weight = 12385.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025274 restraints weight = 12385.444| |-----------------------------------------------------------------------------| r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 1.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.005 1208 Z= 0.109 Angle : 0.345 1.749 1201 Z= 0.282 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.027 14.178 398 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.41), residues: 384 helix: -0.04 (0.36), residues: 213 sheet: None (None), residues: 0 loop : 0.43 (0.45), residues: 171 Details of bonding type rmsd covalent geometry : bond 0.00141 ( 1208) covalent geometry : angle 0.34527 ( 1201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.032 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0039 time to fit residues: 0.0682 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.0070 overall best weight: 7.8010 ------------------------------------------------------------------------------- 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 = 0.2488 r_free = 0.2488 target = 0.032438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.023667 restraints weight = 13964.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.023745 restraints weight = 13159.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.023756 restraints weight = 12556.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.023756 restraints weight = 12479.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.023756 restraints weight = 12479.961| |-----------------------------------------------------------------------------| r_work (final): 0.2162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 1.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 1208 Z= 0.418 Angle : 0.832 4.005 1201 Z= 0.653 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.801 19.682 398 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 44.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.95 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.41), residues: 384 helix: -1.12 (0.40), residues: 155 sheet: None (None), residues: 0 loop : 0.34 (0.40), residues: 229 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 1208) covalent geometry : angle 0.83209 ( 1201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.065 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0083 time to fit residues: 0.2053 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.0470 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.0010 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 overall best weight: 5.6090 ------------------------------------------------------------------------------- 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 = 0.2473 r_free = 0.2473 target = 0.031990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.023085 restraints weight = 13984.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2178 r_free = 0.2178 target = 0.023192 restraints weight = 12633.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.023333 restraints weight = 11782.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.023416 restraints weight = 11075.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.023416 restraints weight = 10573.566| |-----------------------------------------------------------------------------| r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 1.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 1208 Z= 0.309 Angle : 0.679 3.752 1201 Z= 0.538 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.144 18.027 398 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 34.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.42), residues: 384 helix: -1.15 (0.41), residues: 162 sheet: None (None), residues: 0 loop : -0.09 (0.40), residues: 222 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 1208) covalent geometry : angle 0.67898 ( 1201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.055 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0064 time to fit residues: 0.1174 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 overall best weight: 2.4982 ------------------------------------------------------------------------------- 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 = 0.2489 r_free = 0.2489 target = 0.032380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2193 r_free = 0.2193 target = 0.023433 restraints weight = 14006.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2200 r_free = 0.2200 target = 0.023591 restraints weight = 12584.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2205 r_free = 0.2205 target = 0.023696 restraints weight = 11604.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.023769 restraints weight = 10937.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.023771 restraints weight = 10470.667| |-----------------------------------------------------------------------------| r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 1.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.007 1208 Z= 0.155 Angle : 0.430 2.342 1201 Z= 0.349 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.765 15.517 398 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.42), residues: 384 helix: -0.60 (0.39), residues: 192 sheet: None (None), residues: 0 loop : 0.11 (0.44), residues: 192 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 1208) covalent geometry : angle 0.43011 ( 1201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.046 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0041 time to fit residues: 0.0948 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 overall best weight: 0.3002 ------------------------------------------------------------------------------- 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 = 0.2708 r_free = 0.2708 target = 0.037702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.030018 restraints weight = 11152.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.030018 restraints weight = 11041.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.030018 restraints weight = 11042.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.030018 restraints weight = 11042.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.030018 restraints weight = 11042.060| |-----------------------------------------------------------------------------| r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 1.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.003 1208 Z= 0.048 Angle : 0.224 0.907 1201 Z= 0.179 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 3.703 10.562 398 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.44), residues: 384 helix: 0.61 (0.37), residues: 217 sheet: None (None), residues: 0 loop : 0.82 (0.50), residues: 167 Details of bonding type rmsd covalent geometry : bond 0.00062 ( 1208) covalent geometry : angle 0.22391 ( 1201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.060 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0065 time to fit residues: 0.1259 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.0040 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5198 ------------------------------------------------------------------------------- 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 = 0.2540 r_free = 0.2540 target = 0.033003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.024480 restraints weight = 11987.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.024407 restraints weight = 12382.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.024448 restraints weight = 13282.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.024453 restraints weight = 12341.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.024488 restraints weight = 12551.136| |-----------------------------------------------------------------------------| r_work (final): 0.2252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 1.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.009 1208 Z= 0.208 Angle : 0.500 2.700 1201 Z= 0.402 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.798 16.021 398 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.43), residues: 384 helix: 0.51 (0.40), residues: 184 sheet: None (None), residues: 0 loop : 0.71 (0.44), residues: 200 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 1208) covalent geometry : angle 0.49999 ( 1201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.055 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0061 time to fit residues: 0.1148 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0070 chunk 13 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 0.0040 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 overall best weight: 1.9010 ------------------------------------------------------------------------------- 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 = 0.2556 r_free = 0.2556 target = 0.033485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.024923 restraints weight = 12128.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.024664 restraints weight = 12310.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.024608 restraints weight = 14253.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.024644 restraints weight = 13099.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.024662 restraints weight = 12969.836| |-----------------------------------------------------------------------------| r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 1.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.005 1208 Z= 0.122 Angle : 0.357 1.911 1201 Z= 0.291 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.991 14.547 398 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.43), residues: 384 helix: 0.67 (0.41), residues: 181 sheet: None (None), residues: 0 loop : 0.64 (0.43), residues: 203 Details of bonding type rmsd covalent geometry : bond 0.00158 ( 1208) covalent geometry : angle 0.35725 ( 1201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 350.63 seconds wall clock time: 6 minutes 52.07 seconds (412.07 seconds total)