Starting phenix.real_space_refine on Tue Aug 4 11:43:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.cif Found real_map, /net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.map" model { file = "/net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10sg_75434/08_2026/10sg_75434.cif" } resolution = 2.84 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: 3 Type Number sf(0) Gaussians C 826 2.51 5 N 190 2.21 5 O 177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1193 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 59 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 66 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.43, per 1000 atoms: 0.36 Number of scatterers: 1193 At special positions: 0 Unit cell: (93.12, 110.192, 31.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 177 8.00 N 190 7.00 C 826 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.09 Conformation dependent library (CDL) restraints added in 22.7 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... 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: 0.00 Time building geometry restraints manager: 0.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.27: 149 1.27 - 1.34: 114 1.34 - 1.42: 185 1.42 - 1.50: 211 1.50 - 1.58: 537 Bond restraints: 1196 Sorted by residual: bond pdb=" CA SER G 10 " pdb=" CB SER G 10 " ideal model delta sigma weight residual 1.529 1.469 0.061 1.54e-02 4.22e+03 1.56e+01 bond pdb=" CA SER F 10 " pdb=" CB SER F 10 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.90e-02 2.77e+03 1.55e+01 bond pdb=" CA GLY K 8 " pdb=" C GLY K 8 " ideal model delta sigma weight residual 1.517 1.542 -0.024 7.00e-03 2.04e+04 1.19e+01 bond pdb=" CA SER B 10 " pdb=" CB SER B 10 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.57e-02 4.06e+03 1.18e+01 bond pdb=" CA GLY C 8 " pdb=" C GLY C 8 " ideal model delta sigma weight residual 1.516 1.490 0.026 8.10e-03 1.52e+04 1.02e+01 ... (remaining 1191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 1368 2.99 - 5.98: 159 5.98 - 8.97: 11 8.97 - 11.96: 2 11.96 - 14.95: 1 Bond angle restraints: 1541 Sorted by residual: angle pdb=" C LYS E 11 " pdb=" CA LYS E 11 " pdb=" CB LYS E 11 " ideal model delta sigma weight residual 110.10 125.05 -14.95 1.90e+00 2.77e-01 6.19e+01 angle pdb=" N LYS M 11 " pdb=" CA LYS M 11 " pdb=" CB LYS M 11 " ideal model delta sigma weight residual 110.50 119.69 -9.19 1.70e+00 3.46e-01 2.92e+01 angle pdb=" CB LYS M 11 " pdb=" CG LYS M 11 " pdb=" CD LYS M 11 " ideal model delta sigma weight residual 111.30 123.22 -11.92 2.30e+00 1.89e-01 2.69e+01 angle pdb=" N TYR J 3 " pdb=" CA TYR J 3 " pdb=" CB TYR J 3 " ideal model delta sigma weight residual 111.09 116.79 -5.70 1.24e+00 6.50e-01 2.12e+01 angle pdb=" CA GLY C 8 " pdb=" C GLY C 8 " pdb=" O GLY C 8 " ideal model delta sigma weight residual 120.57 116.88 3.69 9.50e-01 1.11e+00 1.51e+01 ... (remaining 1536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.18: 581 11.18 - 22.35: 82 22.35 - 33.52: 29 33.52 - 44.70: 7 44.70 - 55.87: 6 Dihedral angle restraints: 705 sinusoidal: 348 harmonic: 357 Sorted by residual: dihedral pdb=" CA ILE G 7 " pdb=" C ILE G 7 " pdb=" N GLY G 8 " pdb=" CA GLY G 8 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C LYS E 11 " pdb=" N LYS E 11 " pdb=" CA LYS E 11 " pdb=" CB LYS E 11 " ideal model delta harmonic sigma weight residual -122.60 -135.53 12.93 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" CA GLY G 9 " pdb=" C GLY G 9 " pdb=" N SER G 10 " pdb=" CA SER G 10 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 702 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.070: 62 0.070 - 0.137: 65 0.137 - 0.205: 17 0.205 - 0.273: 6 0.273 - 0.340: 2 Chirality restraints: 152 Sorted by residual: chirality pdb=" CA LYS M 11 " pdb=" N LYS M 11 " pdb=" C LYS M 11 " pdb=" CB LYS M 11 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA PRO A 4 " pdb=" N PRO A 4 " pdb=" C PRO A 4 " pdb=" CB PRO A 4 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA LYS E 11 " pdb=" N LYS E 11 " pdb=" C LYS E 11 " pdb=" CB LYS E 11 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 149 not shown) Planarity restraints: 165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 3 " 0.025 2.00e-02 2.50e+03 1.81e-02 6.55e+00 pdb=" CG TYR C 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 3 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 3 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR C 3 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR C 3 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 3 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS M 2 " -0.018 2.00e-02 2.50e+03 2.09e-02 6.55e+00 pdb=" CG HIS M 2 " -0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS M 2 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS M 2 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS M 2 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS M 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 3 " 0.023 2.00e-02 2.50e+03 1.72e-02 5.89e+00 pdb=" CG TYR L 3 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 3 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR L 3 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR L 3 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR L 3 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR L 3 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 3 " 0.006 2.00e-02 2.50e+03 ... (remaining 162 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 531 3.04 - 3.50: 728 3.50 - 3.97: 1484 3.97 - 4.43: 1224 4.43 - 4.90: 1932 Nonbonded interactions: 5899 Sorted by model distance: nonbonded pdb=" O SER L 10 " pdb=" OG SER L 10 " model vdw 2.570 3.040 nonbonded pdb=" N LYS I 11 " pdb=" O LYS I 11 " model vdw 2.629 2.496 nonbonded pdb=" O PRO H 4 " pdb=" N VAL H 6 " model vdw 2.669 3.120 nonbonded pdb=" N GLY L 8 " pdb=" O GLY L 8 " model vdw 2.676 2.496 nonbonded pdb=" N GLY C 8 " pdb=" O GLY C 8 " model vdw 2.677 2.496 ... (remaining 5894 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 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 10)) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.110 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.590 Find NCS groups from input model: 0.040 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:5.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.023 0.197 1220 Z= 2.084 Angle : 1.960 14.952 1541 Z= 1.178 Chirality : 0.108 0.340 152 Planarity : 0.009 0.021 165 Dihedral : 12.662 55.872 485 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 2.75 % Allowed : 4.59 % Favored : 92.66 % Cbeta Deviations : 1.82 % 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 are not related in a simple way. whole: -4.35 (0.60), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.008 TYR E 3 HIS 0.024 0.004 HIS M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.83 ( 1196) covalent geometry : angle 1.95977 / 1.18 ( 1541) Misc. bond : bond 0.13666 / 10.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.028 Fit side-chains revert: symmetry clash REVERT: B 3 TYR cc_start: 0.8456 (m-80) cc_final: 0.7729 (p90) REVERT: D 3 TYR cc_start: 0.8456 (m-80) cc_final: 0.7770 (t80) REVERT: E 3 TYR cc_start: 0.8869 (m-80) cc_final: 0.8348 (p90) REVERT: F 3 TYR cc_start: 0.8928 (m-10) cc_final: 0.8151 (p90) REVERT: H 3 TYR cc_start: 0.7463 (m-10) cc_final: 0.6509 (p90) REVERT: K 3 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: M 3 TYR cc_start: 0.7205 (m-80) cc_final: 0.6368 (t80) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.0922 time to fit residues: 3.6552 Evaluate side-chains 23 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 11 LYS Chi-restraints excluded: chain K residue 3 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 2 HIS E 2 HIS M 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.173648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.151340 restraints weight = 2004.670| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.15 r_work: 0.4179 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1220 Z= 0.237 Angle : 0.641 4.880 1541 Z= 0.280 Chirality : 0.062 0.132 152 Planarity : 0.003 0.018 165 Dihedral : 8.520 37.469 263 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.50 % Allowed : 14.68 % Favored : 79.82 % 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 are not related in a simple way. whole: -2.97 (0.67), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR E 3 HIS 0.007 0.001 HIS M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 ( 1196) covalent geometry : angle 0.64149 / 0.28 ( 1541) Misc. bond : bond 0.00101 / 0.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.029 Fit side-chains revert: symmetry clash REVERT: H 3 TYR cc_start: 0.6249 (m-10) cc_final: 0.5898 (p90) REVERT: M 3 TYR cc_start: 0.6570 (m-80) cc_final: 0.6357 (t80) outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.0757 time to fit residues: 1.9352 Evaluate side-chains 15 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain M residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 0.0030 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.169506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.147913 restraints weight = 2305.256| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.47 r_work: 0.4169 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1220 Z= 0.188 Angle : 0.573 4.041 1541 Z= 0.258 Chirality : 0.061 0.127 152 Planarity : 0.003 0.021 165 Dihedral : 8.231 55.383 257 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.42 % Allowed : 17.43 % Favored : 76.15 % 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 are not related in a simple way. whole: -2.57 (0.69), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 3 HIS 0.003 0.001 HIS L 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 1196) covalent geometry : angle 0.57254 / 0.26 ( 1541) Misc. bond : bond 0.00077 / 0.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: D 3 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.3300 (t80) REVERT: H 3 TYR cc_start: 0.6423 (m-10) cc_final: 0.5795 (p90) REVERT: M 3 TYR cc_start: 0.6663 (m-80) cc_final: 0.6262 (t80) outliers start: 7 outliers final: 6 residues processed: 17 average time/residue: 0.1207 time to fit residues: 2.1826 Evaluate side-chains 17 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain M residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.170273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.148521 restraints weight = 2351.474| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.51 r_work: 0.4182 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1220 Z= 0.120 Angle : 0.470 3.354 1541 Z= 0.206 Chirality : 0.060 0.128 152 Planarity : 0.003 0.023 165 Dihedral : 6.771 47.651 257 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.34 % Allowed : 17.43 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.72), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 1196) covalent geometry : angle 0.46998 / 0.21 ( 1541) Misc. bond : bond 0.00052 / 0.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.057 Fit side-chains REVERT: D 10 SER cc_start: 0.7241 (OUTLIER) cc_final: 0.6748 (m) REVERT: H 3 TYR cc_start: 0.6277 (m-10) cc_final: 0.5688 (p90) outliers start: 8 outliers final: 5 residues processed: 17 average time/residue: 0.0729 time to fit residues: 1.3910 Evaluate side-chains 15 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 8 optimal weight: 0.0040 chunk 10 optimal weight: 0.0770 chunk 5 optimal weight: 0.0270 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.170647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.149118 restraints weight = 2345.140| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.53 r_work: 0.4180 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1220 Z= 0.103 Angle : 0.446 3.280 1541 Z= 0.196 Chirality : 0.060 0.126 152 Planarity : 0.003 0.027 165 Dihedral : 6.164 51.786 257 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.34 % Allowed : 18.35 % Favored : 74.31 % 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 are not related in a simple way. whole: -1.85 (0.72), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 3 HIS 0.001 0.000 HIS L 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 1196) covalent geometry : angle 0.44566 / 0.20 ( 1541) Misc. bond : bond 0.00038 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.048 Fit side-chains REVERT: D 3 TYR cc_start: 0.5950 (OUTLIER) cc_final: 0.3798 (t80) REVERT: D 10 SER cc_start: 0.7257 (OUTLIER) cc_final: 0.6770 (m) REVERT: H 3 TYR cc_start: 0.6234 (m-10) cc_final: 0.5720 (p90) outliers start: 8 outliers final: 5 residues processed: 16 average time/residue: 0.0667 time to fit residues: 1.2046 Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 0.0040 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.170656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.149027 restraints weight = 2371.372| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.56 r_work: 0.4180 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1220 Z= 0.101 Angle : 0.432 3.217 1541 Z= 0.190 Chirality : 0.060 0.125 152 Planarity : 0.003 0.029 165 Dihedral : 6.003 51.349 257 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.26 % Allowed : 19.27 % Favored : 72.48 % 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 are not related in a simple way. whole: -1.67 (0.73), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 1196) covalent geometry : angle 0.43197 / 0.19 ( 1541) Misc. bond : bond 0.00037 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.060 Fit side-chains REVERT: D 3 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.3720 (t80) REVERT: D 10 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6758 (m) REVERT: H 3 TYR cc_start: 0.6253 (m-10) cc_final: 0.5779 (p90) outliers start: 9 outliers final: 6 residues processed: 16 average time/residue: 0.0755 time to fit residues: 1.3673 Evaluate side-chains 19 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.169461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.148801 restraints weight = 2292.087| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.28 r_work: 0.4170 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1220 Z= 0.181 Angle : 0.510 3.560 1541 Z= 0.222 Chirality : 0.061 0.126 152 Planarity : 0.003 0.028 165 Dihedral : 7.109 45.877 257 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.34 % Allowed : 19.27 % Favored : 73.39 % 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 are not related in a simple way. whole: -1.65 (0.71), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 3 HIS 0.002 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 1196) covalent geometry : angle 0.51007 / 0.22 ( 1541) Misc. bond : bond 0.00070 / 0.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 8 time to evaluate : 0.060 Fit side-chains REVERT: B 10 SER cc_start: 0.7205 (t) cc_final: 0.6834 (m) REVERT: D 3 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.3415 (t80) REVERT: D 10 SER cc_start: 0.7146 (OUTLIER) cc_final: 0.6627 (m) REVERT: H 3 TYR cc_start: 0.6259 (m-10) cc_final: 0.5883 (p90) outliers start: 8 outliers final: 6 residues processed: 15 average time/residue: 0.0820 time to fit residues: 1.3852 Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 8 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 11 optimal weight: 6.9990 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.170155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.149506 restraints weight = 2304.446| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 3.29 r_work: 0.4190 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1220 Z= 0.115 Angle : 0.437 3.175 1541 Z= 0.190 Chirality : 0.060 0.124 152 Planarity : 0.003 0.027 165 Dihedral : 6.163 50.289 257 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.34 % Allowed : 20.18 % Favored : 72.48 % 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 are not related in a simple way. whole: -1.56 (0.72), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 1196) covalent geometry : angle 0.43663 / 0.19 ( 1541) Misc. bond : bond 0.00044 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.051 Fit side-chains REVERT: B 10 SER cc_start: 0.7159 (t) cc_final: 0.6795 (m) REVERT: D 3 TYR cc_start: 0.5437 (OUTLIER) cc_final: 0.3371 (t80) REVERT: D 10 SER cc_start: 0.7061 (OUTLIER) cc_final: 0.6585 (m) REVERT: H 3 TYR cc_start: 0.6299 (m-10) cc_final: 0.5836 (p90) outliers start: 8 outliers final: 5 residues processed: 15 average time/residue: 0.0705 time to fit residues: 1.1945 Evaluate side-chains 17 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.170494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.149733 restraints weight = 2342.415| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.35 r_work: 0.4189 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1220 Z= 0.118 Angle : 0.434 3.187 1541 Z= 0.189 Chirality : 0.060 0.125 152 Planarity : 0.003 0.026 165 Dihedral : 5.786 40.226 257 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.42 % Allowed : 20.18 % Favored : 73.39 % 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 are not related in a simple way. whole: -1.50 (0.71), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 1196) covalent geometry : angle 0.43444 / 0.19 ( 1541) Misc. bond : bond 0.00043 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.051 Fit side-chains REVERT: B 10 SER cc_start: 0.7163 (t) cc_final: 0.6833 (m) REVERT: D 3 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.3266 (t80) REVERT: D 10 SER cc_start: 0.6988 (OUTLIER) cc_final: 0.6495 (m) REVERT: H 3 TYR cc_start: 0.6246 (m-10) cc_final: 0.5891 (p90) outliers start: 7 outliers final: 5 residues processed: 14 average time/residue: 0.0622 time to fit residues: 0.9984 Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.169682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.148981 restraints weight = 2283.955| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.33 r_work: 0.4184 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1220 Z= 0.154 Angle : 0.480 3.462 1541 Z= 0.208 Chirality : 0.061 0.125 152 Planarity : 0.003 0.026 165 Dihedral : 6.263 30.088 257 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.42 % Allowed : 20.18 % Favored : 73.39 % 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 are not related in a simple way. whole: -1.50 (0.71), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR E 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 1196) covalent geometry : angle 0.47989 / 0.21 ( 1541) Misc. bond : bond 0.00058 / 0.04 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.051 Fit side-chains REVERT: B 10 SER cc_start: 0.7159 (t) cc_final: 0.6807 (m) REVERT: D 3 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.3374 (t80) REVERT: D 10 SER cc_start: 0.7036 (OUTLIER) cc_final: 0.6492 (m) REVERT: H 3 TYR cc_start: 0.6304 (m-10) cc_final: 0.5942 (p90) outliers start: 7 outliers final: 5 residues processed: 14 average time/residue: 0.0628 time to fit residues: 1.0100 Evaluate side-chains 16 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.0000 overall best weight: 1.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.170763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.149996 restraints weight = 2361.838| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.37 r_work: 0.4194 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1220 Z= 0.092 Angle : 0.411 3.041 1541 Z= 0.180 Chirality : 0.060 0.126 152 Planarity : 0.003 0.027 165 Dihedral : 5.230 29.371 257 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.42 % Allowed : 20.18 % Favored : 73.39 % 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 are not related in a simple way. whole: -1.41 (0.71), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 3 HIS 0.001 0.000 HIS E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 1196) covalent geometry : angle 0.41112 / 0.18 ( 1541) Misc. bond : bond 0.00033 / 0.03 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 614.93 seconds wall clock time: 11 minutes 20.39 seconds (680.39 seconds total)