Starting phenix.real_space_refine on Tue Mar 3 14:50:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.map" model { file = "/net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ps_68593/03_2026/22ps_68593.cif" } resolution = 2.96 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= 0.014 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3870 2.51 5 N 1074 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "B" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 841 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1312 Classifications: {'peptide': 164} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 150} Chain breaks: 4 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 841 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1312 Classifications: {'peptide': 164} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 150} Chain breaks: 4 Time building chain proxies: 1.54, per 1000 atoms: 0.25 Number of scatterers: 6156 At special positions: 0 Unit cell: (141.687, 69.615, 90.909, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1188 8.00 N 1074 7.00 C 3870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 464 " - pdb=" SG CYS F 524 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 379.1 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 8.9% alpha, 50.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.647A pdb=" N GLY A 32 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.682A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 406 through 413 removed outlier: 3.552A pdb=" N GLY C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.647A pdb=" N GLY D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.682A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 350 Processing helix chain 'F' and resid 406 through 413 removed outlier: 3.552A pdb=" N GLY F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 513 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.495A pdb=" N TRP A 37 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 51 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP A 35 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS A 96 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TRP A 111 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG A 98 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.495A pdb=" N TRP A 37 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 51 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP A 35 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.647A pdb=" N LEU B 11 " --> pdb=" O GLU B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.436A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 101 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 355 through 357 Processing sheet with id=AA8, first strand: chain 'C' and resid 373 through 376 Processing sheet with id=AA9, first strand: chain 'C' and resid 444 through 449 removed outlier: 5.846A pdb=" N PHE C 503 " --> pdb=" O ASN C 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 444 through 449 removed outlier: 5.846A pdb=" N PHE C 503 " --> pdb=" O ASN C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.495A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS D 96 " --> pdb=" O TRP D 111 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TRP D 111 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG D 98 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.495A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.647A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.436A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR E 101 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AC1, first strand: chain 'F' and resid 373 through 376 Processing sheet with id=AC2, first strand: chain 'F' and resid 444 through 449 removed outlier: 5.846A pdb=" N PHE F 503 " --> pdb=" O ASN F 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 444 through 449 removed outlier: 5.846A pdb=" N PHE F 503 " --> pdb=" O ASN F 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 483 through 484 300 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2004 1.34 - 1.46: 1598 1.46 - 1.58: 2676 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 6310 Sorted by residual: bond pdb=" N GLN E 104 " pdb=" CA GLN E 104 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.71e+00 bond pdb=" N GLN B 104 " pdb=" CA GLN B 104 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.71e+00 bond pdb=" N PHE B 102 " pdb=" CA PHE B 102 " ideal model delta sigma weight residual 1.454 1.481 -0.028 1.18e-02 7.18e+03 5.50e+00 bond pdb=" N PHE E 102 " pdb=" CA PHE E 102 " ideal model delta sigma weight residual 1.454 1.481 -0.028 1.18e-02 7.18e+03 5.50e+00 bond pdb=" N GLY E 105 " pdb=" CA GLY E 105 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.45e-02 4.76e+03 3.48e+00 ... (remaining 6305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8334 1.81 - 3.62: 196 3.62 - 5.43: 34 5.43 - 7.24: 4 7.24 - 9.05: 2 Bond angle restraints: 8570 Sorted by residual: angle pdb=" CA GLY B 103 " pdb=" C GLY B 103 " pdb=" O GLY B 103 " ideal model delta sigma weight residual 121.18 117.73 3.45 8.80e-01 1.29e+00 1.53e+01 angle pdb=" CA GLY E 103 " pdb=" C GLY E 103 " pdb=" O GLY E 103 " ideal model delta sigma weight residual 121.18 117.73 3.45 8.80e-01 1.29e+00 1.53e+01 angle pdb=" CA ASP B 98 " pdb=" C ASP B 98 " pdb=" O ASP B 98 " ideal model delta sigma weight residual 120.23 116.91 3.32 1.02e+00 9.61e-01 1.06e+01 angle pdb=" CA ASP E 98 " pdb=" C ASP E 98 " pdb=" O ASP E 98 " ideal model delta sigma weight residual 120.23 116.91 3.32 1.02e+00 9.61e-01 1.06e+01 angle pdb=" C ASP B 98 " pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " ideal model delta sigma weight residual 109.26 113.38 -4.12 1.47e+00 4.63e-01 7.86e+00 ... (remaining 8565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 3218 14.34 - 28.69: 320 28.69 - 43.03: 120 43.03 - 57.37: 50 57.37 - 71.72: 18 Dihedral angle restraints: 3726 sinusoidal: 1468 harmonic: 2258 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 55.19 37.81 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 55.19 37.81 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 65.27 27.73 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 3723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 692 0.043 - 0.086: 172 0.086 - 0.130: 56 0.130 - 0.173: 4 0.173 - 0.216: 2 Chirality restraints: 926 Sorted by residual: chirality pdb=" CA PHE B 102 " pdb=" N PHE B 102 " pdb=" C PHE B 102 " pdb=" CB PHE B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PHE E 102 " pdb=" N PHE E 102 " pdb=" C PHE E 102 " pdb=" CB PHE E 102 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL A 38 " pdb=" N VAL A 38 " pdb=" C VAL A 38 " pdb=" CB VAL A 38 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 923 not shown) Planarity restraints: 1102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 97 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C GLU E 97 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU E 97 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP E 98 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 97 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C GLU B 97 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU B 97 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 98 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 83 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 84 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.020 5.00e-02 4.00e+02 ... (remaining 1099 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 214 2.71 - 3.25: 5535 3.25 - 3.80: 10108 3.80 - 4.35: 13240 4.35 - 4.90: 22443 Nonbonded interactions: 51540 Sorted by model distance: nonbonded pdb=" OG SER E 7 " pdb=" CG2 THR E 22 " model vdw 2.157 3.460 nonbonded pdb=" OG SER B 7 " pdb=" CG2 THR B 22 " model vdw 2.157 3.460 nonbonded pdb=" OE1 GLU F 444 " pdb=" OH TYR F 446 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLU C 444 " pdb=" OH TYR C 446 " model vdw 2.251 3.040 nonbonded pdb=" ND1 HIS D 105 " pdb=" O SER E 95 " model vdw 2.266 3.120 ... (remaining 51535 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 3.130 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.003 0.033 6318 Z= 0.168 Angle : 0.697 9.047 8586 Z= 0.381 Chirality : 0.044 0.216 926 Planarity : 0.004 0.035 1102 Dihedral : 15.323 71.717 2250 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.03 (0.31), residues: 758 helix: -1.82 (0.58), residues: 44 sheet: -0.17 (0.27), residues: 350 loop : 0.71 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 431 TYR 0.011 0.001 TYR B 57 PHE 0.015 0.002 PHE A 79 TRP 0.015 0.002 TRP A 35 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6310) covalent geometry : angle 0.69715 ( 8570) SS BOND : bond 0.00234 ( 8) SS BOND : angle 0.74237 ( 16) hydrogen bonds : bond 0.11427 ( 244) hydrogen bonds : angle 7.00892 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.5712 time to fit residues: 52.7212 Evaluate side-chains 72 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 GLN F 518 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.197914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169497 restraints weight = 6893.852| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.24 r_work: 0.3765 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6318 Z= 0.202 Angle : 0.612 6.097 8586 Z= 0.316 Chirality : 0.044 0.154 926 Planarity : 0.004 0.033 1102 Dihedral : 4.692 15.512 854 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.55 % Allowed : 19.64 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: -0.00 (0.31), residues: 758 helix: -1.50 (0.69), residues: 44 sheet: -0.16 (0.27), residues: 340 loop : 0.58 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 351 TYR 0.011 0.002 TYR B 40 PHE 0.015 0.002 PHE D 79 TRP 0.012 0.002 TRP C 516 HIS 0.005 0.002 HIS C 480 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 6310) covalent geometry : angle 0.61135 ( 8570) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.69352 ( 16) hydrogen bonds : bond 0.03631 ( 244) hydrogen bonds : angle 5.69176 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.273 Fit side-chains REVERT: B 3 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: B 43 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7560 (mttp) REVERT: E 3 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: E 43 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7560 (mttp) outliers start: 44 outliers final: 18 residues processed: 118 average time/residue: 0.5084 time to fit residues: 63.1463 Evaluate side-chains 98 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 378 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.199032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170839 restraints weight = 6807.681| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.23 r_work: 0.3789 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6318 Z= 0.162 Angle : 0.556 5.007 8586 Z= 0.288 Chirality : 0.043 0.151 926 Planarity : 0.004 0.035 1102 Dihedral : 4.505 15.500 854 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.25 % Allowed : 22.02 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.04 (0.31), residues: 758 helix: -1.35 (0.68), residues: 44 sheet: -0.15 (0.27), residues: 340 loop : 0.62 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 351 TYR 0.010 0.002 TYR B 36 PHE 0.015 0.002 PHE A 79 TRP 0.014 0.002 TRP A 35 HIS 0.003 0.002 HIS C 490 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6310) covalent geometry : angle 0.55567 ( 8570) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.72575 ( 16) hydrogen bonds : bond 0.03167 ( 244) hydrogen bonds : angle 5.45122 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.262 Fit side-chains REVERT: C 440 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.4556 (tpp80) REVERT: F 440 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.4550 (tpp80) outliers start: 42 outliers final: 20 residues processed: 118 average time/residue: 0.4786 time to fit residues: 59.5654 Evaluate side-chains 98 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 GLN F 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.200595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172301 restraints weight = 6793.710| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.24 r_work: 0.3793 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6318 Z= 0.125 Angle : 0.523 4.931 8586 Z= 0.269 Chirality : 0.041 0.149 926 Planarity : 0.004 0.036 1102 Dihedral : 4.242 14.496 854 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.76 % Allowed : 23.21 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.22 (0.31), residues: 758 helix: -1.29 (0.67), residues: 44 sheet: 0.01 (0.27), residues: 340 loop : 0.70 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 351 TYR 0.010 0.001 TYR B 36 PHE 0.013 0.002 PHE A 79 TRP 0.014 0.002 TRP A 35 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6310) covalent geometry : angle 0.52300 ( 8570) SS BOND : bond 0.00235 ( 8) SS BOND : angle 0.67242 ( 16) hydrogen bonds : bond 0.02833 ( 244) hydrogen bonds : angle 5.18902 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.225 Fit side-chains REVERT: A 118 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6728 (p) REVERT: D 118 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6733 (p) outliers start: 32 outliers final: 16 residues processed: 110 average time/residue: 0.4548 time to fit residues: 52.9824 Evaluate side-chains 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 GLN F 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.200035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171388 restraints weight = 6919.070| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.26 r_work: 0.3791 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6318 Z= 0.134 Angle : 0.524 5.350 8586 Z= 0.270 Chirality : 0.041 0.146 926 Planarity : 0.004 0.036 1102 Dihedral : 4.191 14.078 854 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.95 % Allowed : 22.62 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.26 (0.32), residues: 758 helix: -1.20 (0.67), residues: 44 sheet: 0.03 (0.27), residues: 340 loop : 0.73 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 351 TYR 0.010 0.002 TYR E 36 PHE 0.013 0.002 PHE D 79 TRP 0.013 0.002 TRP C 516 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6310) covalent geometry : angle 0.52354 ( 8570) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.66595 ( 16) hydrogen bonds : bond 0.02827 ( 244) hydrogen bonds : angle 5.16301 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.239 Fit side-chains REVERT: A 118 THR cc_start: 0.7154 (OUTLIER) cc_final: 0.6773 (p) REVERT: B 3 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: B 110 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.4056 (mm) REVERT: C 529 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: D 118 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6782 (p) REVERT: E 3 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: E 110 ILE cc_start: 0.4307 (OUTLIER) cc_final: 0.4048 (mm) REVERT: F 529 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7840 (pm20) outliers start: 40 outliers final: 18 residues processed: 116 average time/residue: 0.4724 time to fit residues: 57.7250 Evaluate side-chains 102 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 GLN F 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169733 restraints weight = 6833.025| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.22 r_work: 0.3774 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6318 Z= 0.170 Angle : 0.570 5.143 8586 Z= 0.292 Chirality : 0.043 0.148 926 Planarity : 0.004 0.034 1102 Dihedral : 4.343 14.258 854 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.55 % Allowed : 23.21 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.18 (0.32), residues: 758 helix: -1.07 (0.68), residues: 44 sheet: -0.07 (0.27), residues: 340 loop : 0.70 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 351 TYR 0.009 0.002 TYR B 36 PHE 0.012 0.002 PHE D 79 TRP 0.013 0.002 TRP C 516 HIS 0.004 0.002 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6310) covalent geometry : angle 0.56919 ( 8570) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.73745 ( 16) hydrogen bonds : bond 0.02997 ( 244) hydrogen bonds : angle 5.31147 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.171 Fit side-chains REVERT: A 118 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6797 (p) REVERT: B 110 ILE cc_start: 0.4303 (OUTLIER) cc_final: 0.4038 (mm) REVERT: C 440 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.4787 (tpp80) REVERT: C 529 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: D 118 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6804 (p) REVERT: E 110 ILE cc_start: 0.4295 (OUTLIER) cc_final: 0.4082 (mm) REVERT: F 440 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.4781 (tpp80) REVERT: F 529 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7822 (pm20) outliers start: 44 outliers final: 22 residues processed: 126 average time/residue: 0.4813 time to fit residues: 63.8641 Evaluate side-chains 110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 1 optimal weight: 0.0370 chunk 73 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 GLN C 518 GLN F 417 GLN F 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.202632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174607 restraints weight = 6844.898| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.21 r_work: 0.3827 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6318 Z= 0.101 Angle : 0.525 5.805 8586 Z= 0.268 Chirality : 0.041 0.146 926 Planarity : 0.004 0.035 1102 Dihedral : 4.038 14.455 854 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.76 % Allowed : 24.40 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.43 (0.32), residues: 758 helix: -0.79 (0.68), residues: 44 sheet: 0.12 (0.28), residues: 338 loop : 0.82 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 351 TYR 0.009 0.001 TYR E 36 PHE 0.011 0.001 PHE D 79 TRP 0.014 0.001 TRP D 35 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6310) covalent geometry : angle 0.52371 ( 8570) SS BOND : bond 0.00225 ( 8) SS BOND : angle 0.99428 ( 16) hydrogen bonds : bond 0.02610 ( 244) hydrogen bonds : angle 4.86130 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.198 Fit side-chains REVERT: A 118 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6832 (p) REVERT: B 37 MET cc_start: 0.7477 (tpt) cc_final: 0.7011 (tpt) REVERT: C 444 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8204 (pt0) REVERT: D 118 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6839 (p) REVERT: E 37 MET cc_start: 0.7487 (tpt) cc_final: 0.7014 (tpt) REVERT: F 444 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8213 (pt0) outliers start: 32 outliers final: 20 residues processed: 106 average time/residue: 0.4407 time to fit residues: 49.5040 Evaluate side-chains 100 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN E 41 GLN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.194143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166035 restraints weight = 7072.066| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.14 r_work: 0.3733 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6318 Z= 0.253 Angle : 0.641 5.814 8586 Z= 0.330 Chirality : 0.045 0.146 926 Planarity : 0.005 0.033 1102 Dihedral : 4.619 14.848 854 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.21 % Allowed : 25.15 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: -0.04 (0.32), residues: 758 helix: -1.41 (0.62), residues: 44 sheet: -0.19 (0.27), residues: 340 loop : 0.55 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.014 0.002 TYR E 40 PHE 0.012 0.002 PHE A 79 TRP 0.013 0.002 TRP D 48 HIS 0.005 0.002 HIS C 480 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 6310) covalent geometry : angle 0.63974 ( 8570) SS BOND : bond 0.00364 ( 8) SS BOND : angle 1.01724 ( 16) hydrogen bonds : bond 0.03398 ( 244) hydrogen bonds : angle 5.62314 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.226 Fit side-chains REVERT: A 118 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6821 (p) REVERT: B 37 MET cc_start: 0.7937 (tpt) cc_final: 0.7699 (tpt) REVERT: C 529 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: D 118 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.6821 (p) REVERT: E 37 MET cc_start: 0.7942 (tpt) cc_final: 0.7705 (tpt) REVERT: F 529 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7848 (pm20) outliers start: 35 outliers final: 25 residues processed: 115 average time/residue: 0.4538 time to fit residues: 55.1026 Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172739 restraints weight = 6857.213| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.16 r_work: 0.3799 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6318 Z= 0.124 Angle : 0.555 5.772 8586 Z= 0.282 Chirality : 0.041 0.145 926 Planarity : 0.004 0.034 1102 Dihedral : 4.235 14.530 854 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.06 % Allowed : 24.70 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.23 (0.32), residues: 758 helix: -1.11 (0.67), residues: 44 sheet: -0.03 (0.27), residues: 338 loop : 0.73 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.011 0.001 TYR B 36 PHE 0.012 0.002 PHE A 79 TRP 0.014 0.001 TRP D 35 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6310) covalent geometry : angle 0.55371 ( 8570) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.00245 ( 16) hydrogen bonds : bond 0.02734 ( 244) hydrogen bonds : angle 5.10185 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.225 Fit side-chains REVERT: A 118 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.6842 (p) REVERT: B 37 MET cc_start: 0.7634 (tpt) cc_final: 0.7374 (tpt) REVERT: D 118 THR cc_start: 0.7224 (OUTLIER) cc_final: 0.6864 (p) REVERT: E 37 MET cc_start: 0.7639 (tpt) cc_final: 0.7373 (tpt) outliers start: 34 outliers final: 24 residues processed: 115 average time/residue: 0.5462 time to fit residues: 65.8526 Evaluate side-chains 103 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169442 restraints weight = 6985.453| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.16 r_work: 0.3773 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6318 Z= 0.145 Angle : 0.571 5.836 8586 Z= 0.293 Chirality : 0.042 0.145 926 Planarity : 0.004 0.033 1102 Dihedral : 4.300 14.651 854 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.91 % Allowed : 25.15 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.23 (0.32), residues: 758 helix: -1.04 (0.67), residues: 44 sheet: -0.03 (0.28), residues: 338 loop : 0.72 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 351 TYR 0.011 0.002 TYR B 36 PHE 0.012 0.002 PHE A 79 TRP 0.013 0.002 TRP F 516 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6310) covalent geometry : angle 0.57023 ( 8570) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.98550 ( 16) hydrogen bonds : bond 0.02851 ( 244) hydrogen bonds : angle 5.12903 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.230 Fit side-chains REVERT: A 118 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6972 (p) REVERT: B 37 MET cc_start: 0.7725 (tpt) cc_final: 0.7242 (tpt) REVERT: C 529 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: D 118 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.6980 (p) REVERT: E 37 MET cc_start: 0.7738 (tpt) cc_final: 0.7255 (tpt) REVERT: F 529 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7784 (pm20) outliers start: 33 outliers final: 27 residues processed: 107 average time/residue: 0.4778 time to fit residues: 53.9840 Evaluate side-chains 109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169189 restraints weight = 7002.813| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.12 r_work: 0.3774 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6318 Z= 0.159 Angle : 0.584 6.051 8586 Z= 0.299 Chirality : 0.043 0.145 926 Planarity : 0.004 0.033 1102 Dihedral : 4.359 15.219 854 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.61 % Allowed : 25.45 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % 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: 0.18 (0.32), residues: 758 helix: -0.96 (0.68), residues: 44 sheet: -0.09 (0.28), residues: 338 loop : 0.71 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 351 TYR 0.010 0.002 TYR B 36 PHE 0.012 0.002 PHE A 79 TRP 0.012 0.002 TRP C 516 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6310) covalent geometry : angle 0.58318 ( 8570) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.01096 ( 16) hydrogen bonds : bond 0.02955 ( 244) hydrogen bonds : angle 5.17690 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.34 seconds wall clock time: 37 minutes 42.60 seconds (2262.60 seconds total)