Starting phenix.real_space_refine on Wed Mar 5 22:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_31083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_31083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_31083.map" model { file = "/net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_31083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7efc_31083/03_2025/7efc_31083.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, 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: 2.68, per 1000 atoms: 0.67 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: 0.98 Conformation dependent library (CDL) restraints added in 889.4 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: 0.49 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: 1.05 Time building geometry restraints manager: 1.17 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: 2008 16.54 - 33.08: 160 33.08 - 49.62: 20 49.62 - 66.16: 12 66.16 - 82.70: 12 Dihedral angle restraints: 2212 sinusoidal: 788 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 2209 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.130 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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= 2.151 Angle : 3.162 13.316 5400 Z= 2.201 Chirality : 0.090 0.401 604 Planarity : 0.016 0.215 684 Dihedral : 14.879 82.705 1324 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP C 92 HIS 0.001 0.000 HIS C 127 PHE 0.002 0.001 PHE D 130 TYR 0.002 0.001 TYR B 60 ARG 0.000 0.000 ARG D 53 *********************** 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 : 0.377 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: 1.0775 time to fit residues: 71.5807 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 : 0.381 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.166191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137396 restraints weight = 7990.533| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.83 r_work: 0.3655 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 3944 Z= 0.573 Angle : 1.453 16.919 5400 Z= 0.811 Chirality : 0.075 0.448 604 Planarity : 0.014 0.100 684 Dihedral : 9.731 59.186 636 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.18 % Favored : 96.40 % Rotamer: Outliers : 1.61 % Allowed : 8.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.33), residues: 512 helix: -4.94 (0.28), residues: 24 sheet: -0.18 (0.27), residues: 264 loop : -1.63 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.008 TRP B 21 HIS 0.020 0.003 HIS C 87 PHE 0.111 0.019 PHE B 29 TYR 0.224 0.013 TYR B 43 ARG 0.046 0.004 ARG B 53 *********************** 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 : 0.358 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: 1.2705 time to fit residues: 77.4131 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.162401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138627 restraints weight = 4369.710| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.28 r_work: 0.3684 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3944 Z= 0.218 Angle : 0.715 7.192 5400 Z= 0.386 Chirality : 0.044 0.149 604 Planarity : 0.004 0.021 684 Dihedral : 7.568 54.503 632 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.61 % Rotamer: Outliers : 0.81 % Allowed : 6.99 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.34), residues: 512 helix: -5.10 (0.18), residues: 24 sheet: 0.02 (0.24), residues: 316 loop : -0.49 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 92 HIS 0.004 0.002 HIS C 87 PHE 0.023 0.004 PHE A 29 TYR 0.017 0.002 TYR D 43 ARG 0.004 0.001 ARG D 103 *********************** 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 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6878 (mt-10) outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 1.2823 time to fit residues: 83.5198 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 47 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.160911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136772 restraints weight = 4279.327| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.27 r_work: 0.3654 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.23 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 = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3944 Z= 0.389 Angle : 0.829 8.829 5400 Z= 0.454 Chirality : 0.049 0.147 604 Planarity : 0.005 0.036 684 Dihedral : 8.394 43.567 632 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.24 % Favored : 95.55 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.29 (0.25), residues: 296 loop : 0.47 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 92 HIS 0.008 0.003 HIS C 87 PHE 0.027 0.004 PHE D 29 TYR 0.018 0.003 TYR D 43 ARG 0.008 0.002 ARG A 84 *********************** 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 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6928 (mt-10) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 1.4682 time to fit residues: 77.1540 Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.161542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137137 restraints weight = 4474.394| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.32 r_work: 0.3657 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3944 Z= 0.250 Angle : 0.694 8.630 5400 Z= 0.376 Chirality : 0.045 0.156 604 Planarity : 0.004 0.025 684 Dihedral : 7.666 43.370 632 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.27 % Allowed : 9.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.44 (0.25), residues: 296 loop : 0.70 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.020 0.003 PHE D 29 TYR 0.015 0.002 TYR C 22 ARG 0.005 0.001 ARG B 103 *********************** 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 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6768 (mt-10) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 1.5356 time to fit residues: 75.8999 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 7.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136328 restraints weight = 3903.797| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.21 r_work: 0.3642 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3944 Z= 0.463 Angle : 0.835 9.651 5400 Z= 0.464 Chirality : 0.050 0.154 604 Planarity : 0.005 0.041 684 Dihedral : 8.730 42.143 632 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.33 (0.25), residues: 296 loop : 0.53 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP D 92 HIS 0.009 0.004 HIS C 87 PHE 0.017 0.004 PHE D 29 TYR 0.013 0.003 TYR D 43 ARG 0.009 0.003 ARG A 84 *********************** 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 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6882 (mt-10) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 1.4489 time to fit residues: 76.1491 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.4082 r_free = 0.4082 target = 0.164096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140262 restraints weight = 4438.990| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.31 r_work: 0.3697 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3944 Z= 0.146 Angle : 0.593 8.389 5400 Z= 0.316 Chirality : 0.042 0.158 604 Planarity : 0.003 0.019 684 Dihedral : 6.596 44.048 632 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.27 % Allowed : 9.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.33), residues: 512 helix: -5.26 (0.15), residues: 24 sheet: 0.66 (0.25), residues: 296 loop : -0.16 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 108 HIS 0.002 0.001 HIS C 87 PHE 0.011 0.002 PHE D 29 TYR 0.006 0.001 TYR C 22 ARG 0.003 0.000 ARG B 103 *********************** 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 : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6527 (mt-10) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 1.5288 time to fit residues: 75.5403 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 : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 0.0060 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.160353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136931 restraints weight = 3947.226| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.22 r_work: 0.3649 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3944 Z= 0.356 Angle : 0.765 9.565 5400 Z= 0.415 Chirality : 0.049 0.159 604 Planarity : 0.004 0.031 684 Dihedral : 8.056 45.445 632 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.47 (0.25), residues: 296 loop : 0.72 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 92 HIS 0.007 0.003 HIS C 87 PHE 0.007 0.003 PHE D 29 TYR 0.017 0.003 TYR C 22 ARG 0.006 0.002 ARG A 84 *********************** 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 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6776 (mt-10) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 1.5656 time to fit residues: 75.7805 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.161568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137257 restraints weight = 4556.236| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.33 r_work: 0.3654 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 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 = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3330 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= 0.231 Angle : 0.690 9.190 5400 Z= 0.364 Chirality : 0.045 0.159 604 Planarity : 0.003 0.022 684 Dihedral : 7.218 46.253 632 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.33), residues: 512 helix: -5.24 (0.15), residues: 24 sheet: 0.51 (0.25), residues: 296 loop : -0.21 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 108 HIS 0.003 0.002 HIS C 87 PHE 0.007 0.002 PHE A 29 TYR 0.017 0.002 TYR C 22 ARG 0.006 0.001 ARG B 103 *********************** 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 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6651 (mt-10) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.5378 time to fit residues: 77.5186 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.162911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138767 restraints weight = 4613.832| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.32 r_work: 0.3672 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.184 Angle : 0.661 8.465 5400 Z= 0.343 Chirality : 0.044 0.162 604 Planarity : 0.003 0.018 684 Dihedral : 7.030 47.784 632 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.33), residues: 512 helix: -5.24 (0.15), residues: 24 sheet: 0.61 (0.26), residues: 296 loop : -0.11 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.002 0.001 HIS C 87 PHE 0.005 0.002 PHE C 29 TYR 0.015 0.001 TYR C 22 ARG 0.015 0.001 ARG B 103 ********************** 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 : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6572 (mt-10) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 1.6731 time to fit residues: 79.4951 Evaluate side-chains 43 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.0000 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.9190 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.161440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137817 restraints weight = 4146.692| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.25 r_work: 0.3659 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 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 = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3354 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= 0.288 Angle : 0.721 9.489 5400 Z= 0.386 Chirality : 0.047 0.158 604 Planarity : 0.004 0.028 684 Dihedral : 7.490 48.002 632 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.33), residues: 512 helix: -5.24 (0.15), residues: 24 sheet: 0.52 (0.25), residues: 296 loop : -0.14 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.006 0.002 PHE B 29 TYR 0.019 0.002 TYR C 22 ARG 0.017 0.002 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5001.22 seconds wall clock time: 85 minutes 57.89 seconds (5157.89 seconds total)