Starting phenix.real_space_refine on Wed Jul 1 23:07:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.cif" model { file = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7efc_31083/07_2026/7efc_31083.map" } resolution = 1.7 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= 0.001 sd= 0.008 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 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} bond proxies already assigned to first conformer: 867 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 40, 55 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 39} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O AHOH A5221 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5231 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 1.01, per 1000 atoms: 0.25 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 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 4 16.00 O 940 8.00 N 668 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 187.3 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 3.3% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 71 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY A 94 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 73 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP A 92 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP A 75 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 90 " --> pdb=" O TRP A 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 77 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER A 88 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP A 79 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 71 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 94 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 73 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP B 92 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP B 75 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 90 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 77 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER B 88 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP B 79 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 71 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 94 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 73 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP C 92 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP C 75 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 90 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL C 77 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER C 88 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP C 79 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR D 71 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY D 94 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 73 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP D 92 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP D 75 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR D 90 " --> pdb=" O TRP D 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 77 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER D 88 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP D 79 " --> pdb=" O ALA D 86 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 456 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: 0.70 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 548 1.29 - 1.42: 880 1.42 - 1.55: 2192 1.55 - 1.68: 316 1.68 - 1.81: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY B 94 " pdb=" O GLY B 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C ILE C 17 " pdb=" O ILE C 17 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.19e-02 7.06e+03 4.86e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 3396 2.66 - 5.33: 1508 5.33 - 7.99: 428 7.99 - 10.65: 44 10.65 - 13.32: 24 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.38 10.47 1.06e+00 8.90e-01 9.75e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 1952 16.54 - 33.08: 156 33.08 - 49.62: 20 49.62 - 66.16: 12 66.16 - 82.70: 12 Dihedral angle restraints: 2152 sinusoidal: 728 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASER A 52 " pdb=" C ASER A 52 " pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 2149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 412 0.080 - 0.160: 164 0.160 - 0.241: 20 0.241 - 0.321: 0 0.321 - 0.401: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL A 31 " pdb=" CA VAL A 31 " pdb=" CG1 VAL A 31 " pdb=" CG2 VAL A 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL C 31 " pdb=" CA VAL C 31 " pdb=" CG1 VAL C 31 " pdb=" CG2 VAL C 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL B 31 " pdb=" CA VAL B 31 " pdb=" CG1 VAL B 31 " pdb=" CG2 VAL B 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN C5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN C5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN C5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN C5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.262 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1438 2.94 - 3.92: 11594 3.92 - 4.90: 22880 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35914 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 3.040 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 3.040 nonbonded pdb=" O AASN C 49 " pdb=" OD1AASN C 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.057 3.040 ... (remaining 35909 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.94 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: 0.180 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.890 Find NCS groups from input model: 0.040 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:9.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.032 0.090 3944 Z= 2.144 Angle : 3.162 13.316 5400 Z= 2.201 Chirality : 0.090 0.401 604 Planarity : 0.016 0.215 684 Dihedral : 15.028 82.705 1264 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 3.60 % 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: -0.84 (0.33), residues: 512 helix: None (None), residues: 0 sheet: 0.30 (0.29), residues: 244 loop : -1.41 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 53 TYR 0.002 0.001 TYR B 60 PHE 0.002 0.001 PHE D 130 TRP 0.004 0.001 TRP C 92 HIS 0.001 0.000 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.03226 / 2.14 ( 3944) covalent geometry : angle 3.16201 / 2.20 ( 5400) hydrogen bonds : bond 0.13857 / 9.04 ( 168) hydrogen bonds : angle 9.73459 / 6.77 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8217 (m) cc_final: 0.7789 (p) REVERT: A 53 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: A 69 SER cc_start: 0.7845 (m) cc_final: 0.7634 (t) REVERT: A 103 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7435 (mtm-85) REVERT: B 27 SER cc_start: 0.8218 (m) cc_final: 0.7790 (p) REVERT: B 53 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7499 (ttp80) REVERT: B 69 SER cc_start: 0.7845 (m) cc_final: 0.7635 (t) REVERT: B 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7434 (mtm-85) REVERT: C 27 SER cc_start: 0.8215 (m) cc_final: 0.7788 (p) REVERT: C 53 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: C 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: C 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7433 (mtm-85) REVERT: D 27 SER cc_start: 0.8217 (m) cc_final: 0.7788 (p) REVERT: D 53 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7500 (ttp80) REVERT: D 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: D 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7435 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.5672 time to fit residues: 37.5118 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.167986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139401 restraints weight = 8099.555| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.83 r_work: 0.3677 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 3944 Z= 0.382 Angle : 1.400 18.746 5400 Z= 0.779 Chirality : 0.071 0.457 604 Planarity : 0.013 0.097 684 Dihedral : 9.687 58.810 576 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.97 % Rotamer: Outliers : 1.61 % Allowed : 8.60 % Favored : 89.78 % Cbeta Deviations : 0.23 % 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: -1.84 (0.33), residues: 512 helix: -4.85 (0.28), residues: 24 sheet: -0.51 (0.26), residues: 276 loop : -1.63 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.003 ARG B 53 TYR 0.180 0.011 TYR B 43 PHE 0.123 0.019 PHE B 29 TRP 0.075 0.007 TRP B 108 HIS 0.025 0.003 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.38 ( 3944) covalent geometry : angle 1.40046 / 0.78 ( 5400) hydrogen bonds : bond 0.06610 / 4.37 ( 168) hydrogen bonds : angle 8.90265 / 6.27 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 59 average time/residue: 0.6212 time to fit residues: 37.7415 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139725 restraints weight = 3738.228| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.17 r_work: 0.3700 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3944 Z= 0.178 Angle : 0.721 6.797 5400 Z= 0.391 Chirality : 0.044 0.147 604 Planarity : 0.004 0.021 684 Dihedral : 7.754 52.289 572 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.60 % Favored : 96.19 % Rotamer: Outliers : 0.81 % Allowed : 7.53 % Favored : 91.67 % 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: 0.22 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.27 (0.24), residues: 304 loop : 0.15 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 103 TYR 0.016 0.002 TYR B 22 PHE 0.023 0.003 PHE A 29 TRP 0.020 0.003 TRP D 75 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 3944) covalent geometry : angle 0.72143 / 0.39 ( 5400) hydrogen bonds : bond 0.04669 / 3.26 ( 168) hydrogen bonds : angle 8.01003 / 5.67 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6883 (mt-10) outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.5241 time to fit residues: 34.1875 Evaluate side-chains 58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.162187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138003 restraints weight = 4180.821| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.27 r_work: 0.3669 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3944 Z= 0.185 Angle : 0.728 8.685 5400 Z= 0.385 Chirality : 0.045 0.152 604 Planarity : 0.004 0.021 684 Dihedral : 7.573 41.090 572 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 10.22 % Favored : 89.52 % 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: 0.58 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.39 (0.25), residues: 296 loop : 0.60 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 103 TYR 0.016 0.002 TYR C 22 PHE 0.023 0.003 PHE D 29 TRP 0.015 0.003 TRP D 75 HIS 0.004 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 3944) covalent geometry : angle 0.72825 / 0.39 ( 5400) hydrogen bonds : bond 0.04952 / 3.46 ( 168) hydrogen bonds : angle 7.75790 / 5.45 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6788 (mt-10) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.6362 time to fit residues: 31.3572 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.160998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136900 restraints weight = 4186.006| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.27 r_work: 0.3652 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3944 Z= 0.244 Angle : 0.758 9.156 5400 Z= 0.410 Chirality : 0.047 0.168 604 Planarity : 0.004 0.032 684 Dihedral : 7.933 43.602 572 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.81 % Allowed : 9.41 % Favored : 89.78 % 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: 0.57 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.38 (0.25), residues: 296 loop : 0.61 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG A 84 TYR 0.016 0.002 TYR C 22 PHE 0.020 0.004 PHE D 29 TRP 0.015 0.003 TRP D 92 HIS 0.005 0.003 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 ( 3944) covalent geometry : angle 0.75833 / 0.41 ( 5400) hydrogen bonds : bond 0.05594 / 3.86 ( 168) hydrogen bonds : angle 7.79983 / 5.46 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6808 (mt-10) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.6441 time to fit residues: 32.4356 Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.163384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139106 restraints weight = 4448.247| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.32 r_work: 0.3682 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3944 Z= 0.126 Angle : 0.623 8.304 5400 Z= 0.329 Chirality : 0.043 0.162 604 Planarity : 0.003 0.022 684 Dihedral : 6.900 39.721 572 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.08 % Allowed : 8.87 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.33), residues: 512 helix: -5.24 (0.15), residues: 24 sheet: 0.59 (0.25), residues: 296 loop : -0.08 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.013 0.001 TYR C 22 PHE 0.010 0.002 PHE A 29 TRP 0.012 0.002 TRP B 108 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 3944) covalent geometry : angle 0.62334 / 0.33 ( 5400) hydrogen bonds : bond 0.04678 / 3.30 ( 168) hydrogen bonds : angle 7.28012 / 5.10 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6673 (mt-10) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.6244 time to fit residues: 32.7649 Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.161276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137237 restraints weight = 4283.848| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.28 r_work: 0.3654 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3944 Z= 0.227 Angle : 0.733 9.154 5400 Z= 0.394 Chirality : 0.047 0.160 604 Planarity : 0.004 0.027 684 Dihedral : 7.869 39.455 572 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.27 % Allowed : 9.68 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.45 (0.25), residues: 296 loop : 0.80 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 84 TYR 0.012 0.002 TYR C 22 PHE 0.009 0.002 PHE D 29 TRP 0.014 0.003 TRP B 92 HIS 0.005 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 ( 3944) covalent geometry : angle 0.73252 / 0.39 ( 5400) hydrogen bonds : bond 0.05498 / 3.78 ( 168) hydrogen bonds : angle 7.71009 / 5.39 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6776 (mt-10) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.6565 time to fit residues: 33.0658 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.161526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137835 restraints weight = 4070.027| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.25 r_work: 0.3661 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3944 Z= 0.190 Angle : 0.704 9.028 5400 Z= 0.374 Chirality : 0.046 0.160 604 Planarity : 0.004 0.021 684 Dihedral : 7.610 40.707 572 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.81 % Allowed : 9.41 % Favored : 89.78 % 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: -0.22 (0.33), residues: 512 helix: -5.24 (0.15), residues: 24 sheet: 0.45 (0.25), residues: 296 loop : -0.24 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.011 0.002 TYR C 22 PHE 0.006 0.002 PHE A 29 TRP 0.013 0.003 TRP B 92 HIS 0.004 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 3944) covalent geometry : angle 0.70441 / 0.37 ( 5400) hydrogen bonds : bond 0.05230 / 3.63 ( 168) hydrogen bonds : angle 7.56718 / 5.29 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6685 (mt-10) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.6404 time to fit residues: 35.6295 Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.160669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136973 restraints weight = 4092.742| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.25 r_work: 0.3652 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3944 Z= 0.247 Angle : 0.768 9.427 5400 Z= 0.411 Chirality : 0.048 0.188 604 Planarity : 0.004 0.023 684 Dihedral : 8.028 38.231 572 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % 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: 0.59 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.39 (0.25), residues: 296 loop : 0.63 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 84 TYR 0.010 0.002 TYR C 22 PHE 0.005 0.002 PHE B 29 TRP 0.014 0.003 TRP B 92 HIS 0.005 0.003 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.25 ( 3944) covalent geometry : angle 0.76774 / 0.41 ( 5400) hydrogen bonds : bond 0.05735 / 3.93 ( 168) hydrogen bonds : angle 7.80782 / 5.45 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6801 (mt-10) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.6839 time to fit residues: 32.9881 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.160617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136662 restraints weight = 4271.712| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.28 r_work: 0.3647 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3944 Z= 0.254 Angle : 0.777 9.938 5400 Z= 0.414 Chirality : 0.048 0.160 604 Planarity : 0.004 0.023 684 Dihedral : 8.014 38.739 572 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % 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: -0.35 (0.33), residues: 512 helix: -5.21 (0.15), residues: 24 sheet: 0.38 (0.25), residues: 296 loop : -0.37 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 84 TYR 0.009 0.002 TYR B 96 PHE 0.006 0.002 PHE B 29 TRP 0.015 0.003 TRP B 92 HIS 0.005 0.003 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.25 ( 3944) covalent geometry : angle 0.77677 / 0.41 ( 5400) hydrogen bonds : bond 0.05733 / 3.92 ( 168) hydrogen bonds : angle 7.81696 / 5.45 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6807 (mt-10) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.6908 time to fit residues: 32.6821 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140101 restraints weight = 6234.426| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.56 r_work: 0.3701 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3944 Z= 0.105 Angle : 0.620 8.905 5400 Z= 0.315 Chirality : 0.043 0.160 604 Planarity : 0.003 0.020 684 Dihedral : 6.309 33.932 572 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % 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: 0.09 (0.34), residues: 512 helix: -5.26 (0.16), residues: 24 sheet: 0.76 (0.26), residues: 296 loop : -0.20 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.005 0.001 TYR B 22 PHE 0.007 0.002 PHE B 29 TRP 0.015 0.002 TRP B 108 HIS 0.001 0.000 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 3944) covalent geometry : angle 0.62023 / 0.32 ( 5400) hydrogen bonds : bond 0.04321 / 3.07 ( 168) hydrogen bonds : angle 6.99113 / 4.88 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.56 seconds wall clock time: 40 minutes 15.71 seconds (2415.71 seconds total)