Starting phenix.real_space_refine on Thu Jun 5 11:59:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.map" model { file = "/net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qhs_18416/06_2025/8qhs_18416.cif" } resolution = 2.3 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= 0.055 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 30 5.16 5 C 3725 2.51 5 N 935 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6212 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Restraints were copied for chains: C, E, D, F Time building chain proxies: 4.22, per 1000 atoms: 0.68 Number of scatterers: 6212 At special positions: 0 Unit cell: (72.688, 99.12, 159.418, 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 30 16.00 O 1522 8.00 N 935 7.00 C 3725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS C 104 " distance=3.00 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: 1.56 Conformation dependent library (CDL) restraints added in 928.6 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 14.1% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.514A pdb=" N ASN A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'C' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU C 7 " --> pdb=" O PHE C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 7' Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU D 7 " --> pdb=" O PHE D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 7' Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU E 7 " --> pdb=" O PHE E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU F 7 " --> pdb=" O PHE F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 87 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 38 current: chain 'A' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 82 current: chain 'A' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS A 141 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 126 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 139 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 128 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 137 " --> pdb=" O PHE A 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 137 through 144 current: chain 'D' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 36 through 38 current: chain 'D' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 82 current: chain 'D' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS D 141 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 126 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER D 139 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE D 128 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR D 137 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 38 current: chain 'C' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 82 current: chain 'C' and resid 114 through 129 removed outlier: 6.282A pdb=" N LYS C 141 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 126 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 139 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 128 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 137 " --> pdb=" O PHE C 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 137 through 144 current: chain 'E' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 38 current: chain 'E' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 82 current: chain 'E' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS E 141 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR E 126 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER E 139 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 128 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR E 137 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 36 through 38 current: chain 'F' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 82 current: chain 'F' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS F 141 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 126 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 139 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE F 128 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR F 137 " --> pdb=" O PHE F 128 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 1.41 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1915 1.34 - 1.45: 1011 1.45 - 1.57: 2989 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5965 Sorted by residual: bond pdb=" C ILE D 56 " pdb=" O ILE D 56 " ideal model delta sigma weight residual 1.236 1.223 0.014 1.19e-02 7.06e+03 1.31e+00 bond pdb=" N GLY C 44 " pdb=" CA GLY C 44 " ideal model delta sigma weight residual 1.454 1.443 0.011 9.90e-03 1.02e+04 1.29e+00 bond pdb=" C ILE C 56 " pdb=" O ILE C 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 bond pdb=" C ILE A 56 " pdb=" O ILE A 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 bond pdb=" C ILE E 56 " pdb=" O ILE E 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 ... (remaining 5960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 6889 0.91 - 1.82: 977 1.82 - 2.73: 114 2.73 - 3.64: 40 3.64 - 4.55: 15 Bond angle restraints: 8035 Sorted by residual: angle pdb=" C SER E 112 " pdb=" N LYS E 113 " pdb=" CA LYS E 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER C 112 " pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta sigma weight residual 122.19 125.28 -3.09 1.41e+00 5.03e-01 4.80e+00 angle pdb=" C SER D 112 " pdb=" N LYS D 113 " pdb=" CA LYS D 113 " ideal model delta sigma weight residual 122.19 125.27 -3.08 1.41e+00 5.03e-01 4.76e+00 angle pdb=" C SER F 112 " pdb=" N LYS F 113 " pdb=" CA LYS F 113 " ideal model delta sigma weight residual 122.19 125.26 -3.07 1.41e+00 5.03e-01 4.75e+00 ... (remaining 8030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3160 16.62 - 33.24: 202 33.24 - 49.85: 101 49.85 - 66.47: 55 66.47 - 83.09: 20 Dihedral angle restraints: 3538 sinusoidal: 1333 harmonic: 2205 Sorted by residual: dihedral pdb=" CA ALA F 121 " pdb=" C ALA F 121 " pdb=" N ILE F 122 " pdb=" CA ILE F 122 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA A 121 " pdb=" C ALA A 121 " pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA D 121 " pdb=" C ALA D 121 " pdb=" N ILE D 122 " pdb=" CA ILE D 122 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 453 0.028 - 0.055: 257 0.055 - 0.083: 115 0.083 - 0.110: 50 0.110 - 0.138: 20 Chirality restraints: 895 Sorted by residual: chirality pdb=" CA ILE F 122 " pdb=" N ILE F 122 " pdb=" C ILE F 122 " pdb=" CB ILE F 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 122 " pdb=" N ILE E 122 " pdb=" C ILE E 122 " pdb=" CB ILE E 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 892 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 101 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO E 102 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 101 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 101 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO F 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " -0.016 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 215 2.65 - 3.21: 5559 3.21 - 3.78: 10780 3.78 - 4.34: 14721 4.34 - 4.90: 22938 Nonbonded interactions: 54213 Sorted by model distance: nonbonded pdb=" OD1 ASP E 60 " pdb=" O HOH E 201 " model vdw 2.089 3.040 nonbonded pdb=" O HOH C 222 " pdb=" O HOH C 243 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP F 150 " pdb=" OG1 THR F 152 " model vdw 2.158 3.040 nonbonded pdb=" OD1 ASP D 150 " pdb=" OG1 THR D 152 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP C 150 " pdb=" OG1 THR C 152 " model vdw 2.159 3.040 ... (remaining 54208 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.150 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.014 0.967 5966 Z= 0.693 Angle : 0.688 8.800 8037 Z= 0.407 Chirality : 0.045 0.138 895 Planarity : 0.003 0.028 1035 Dihedral : 17.608 83.088 2135 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.56 % Allowed : 6.56 % Favored : 86.89 % 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: -0.18 (0.27), residues: 765 helix: -0.27 (0.50), residues: 70 sheet: 0.11 (0.29), residues: 290 loop : -0.15 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP D 75 HIS 0.005 0.003 HIS E 90 PHE 0.015 0.002 PHE D 128 TYR 0.006 0.002 TYR F 138 ARG 0.000 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.15643 ( 71) hydrogen bonds : angle 5.38717 ( 213) SS BOND : bond 0.96731 ( 1) SS BOND : angle 8.14900 ( 2) covalent geometry : bond 0.00645 ( 5965) covalent geometry : angle 0.67646 ( 8035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.759 Fit side-chains REVERT: C 17 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6800 (ttpt) REVERT: C 145 MET cc_start: 0.9166 (mtp) cc_final: 0.8881 (mtp) REVERT: E 17 LYS cc_start: 0.7917 (ttmt) cc_final: 0.6997 (ttpt) REVERT: F 145 MET cc_start: 0.9120 (mtp) cc_final: 0.8795 (mtp) outliers start: 40 outliers final: 1 residues processed: 141 average time/residue: 1.5548 time to fit residues: 227.1986 Evaluate side-chains 96 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 159 GLN C 43 GLN C 159 GLN D 43 GLN D 159 GLN E 43 GLN E 159 GLN F 43 GLN F 159 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107805 restraints weight = 5783.150| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.17 r_work: 0.3075 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5966 Z= 0.100 Angle : 0.413 3.010 8037 Z= 0.236 Chirality : 0.043 0.147 895 Planarity : 0.002 0.018 1035 Dihedral : 4.993 52.049 812 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.82 % Allowed : 13.11 % Favored : 86.07 % 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: 0.51 (0.28), residues: 765 helix: 2.09 (0.65), residues: 70 sheet: 0.25 (0.30), residues: 290 loop : 0.22 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.014 0.001 PHE C 128 TYR 0.004 0.001 TYR A 83 ARG 0.002 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02465 ( 71) hydrogen bonds : angle 3.88726 ( 213) SS BOND : bond 0.00745 ( 1) SS BOND : angle 0.17495 ( 2) covalent geometry : bond 0.00221 ( 5965) covalent geometry : angle 0.41292 ( 8035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.669 Fit side-chains REVERT: C 17 LYS cc_start: 0.7987 (ttmt) cc_final: 0.6750 (ttpt) REVERT: C 145 MET cc_start: 0.9314 (mtp) cc_final: 0.9003 (mtp) REVERT: D 129 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: E 17 LYS cc_start: 0.7882 (ttmt) cc_final: 0.6733 (ttpt) REVERT: F 113 LYS cc_start: 0.8549 (mtmm) cc_final: 0.7840 (mptp) outliers start: 5 outliers final: 0 residues processed: 103 average time/residue: 1.7441 time to fit residues: 185.6731 Evaluate side-chains 104 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112907 restraints weight = 5881.451| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.04 r_work: 0.3069 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5966 Z= 0.108 Angle : 0.401 3.073 8037 Z= 0.228 Chirality : 0.043 0.146 895 Planarity : 0.002 0.016 1035 Dihedral : 4.469 16.355 810 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.64 % Allowed : 13.11 % Favored : 85.25 % 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: 0.85 (0.29), residues: 765 helix: 2.53 (0.66), residues: 70 sheet: 0.37 (0.30), residues: 290 loop : 0.51 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.011 0.001 PHE C 128 TYR 0.005 0.001 TYR A 83 ARG 0.001 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.02312 ( 71) hydrogen bonds : angle 3.77996 ( 213) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.16430 ( 2) covalent geometry : bond 0.00240 ( 5965) covalent geometry : angle 0.40094 ( 8035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.852 Fit side-chains REVERT: C 5 GLU cc_start: 0.8193 (mp0) cc_final: 0.7606 (mp0) REVERT: C 17 LYS cc_start: 0.7923 (ttmt) cc_final: 0.6729 (ttpt) REVERT: C 114 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8687 (mmmt) REVERT: D 129 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: E 17 LYS cc_start: 0.7883 (ttmt) cc_final: 0.6788 (ttpt) REVERT: E 129 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: F 113 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8003 (mptp) outliers start: 10 outliers final: 2 residues processed: 108 average time/residue: 1.9406 time to fit residues: 216.7315 Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.121159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103099 restraints weight = 5881.224| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.18 r_work: 0.3003 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5966 Z= 0.261 Angle : 0.567 4.306 8037 Z= 0.312 Chirality : 0.047 0.160 895 Planarity : 0.003 0.024 1035 Dihedral : 5.341 20.595 810 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.80 % Allowed : 13.61 % Favored : 84.59 % 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: 0.84 (0.29), residues: 765 helix: 2.04 (0.62), residues: 70 sheet: 0.35 (0.30), residues: 290 loop : 0.61 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 75 HIS 0.005 0.003 HIS A 90 PHE 0.018 0.002 PHE C 128 TYR 0.009 0.003 TYR A 138 ARG 0.002 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 71) hydrogen bonds : angle 4.19930 ( 213) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.08522 ( 2) covalent geometry : bond 0.00588 ( 5965) covalent geometry : angle 0.56692 ( 8035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.696 Fit side-chains REVERT: C 5 GLU cc_start: 0.8207 (mp0) cc_final: 0.7640 (mp0) REVERT: C 17 LYS cc_start: 0.7991 (ttmt) cc_final: 0.6708 (ttpt) REVERT: C 114 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8862 (mmmt) REVERT: C 129 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: E 17 LYS cc_start: 0.8032 (ttmt) cc_final: 0.6860 (ttpp) REVERT: E 113 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8330 (mppt) REVERT: E 129 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8434 (tp30) REVERT: F 113 LYS cc_start: 0.8636 (mtmm) cc_final: 0.7855 (mptp) outliers start: 11 outliers final: 1 residues processed: 110 average time/residue: 1.8074 time to fit residues: 205.3525 Evaluate side-chains 109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113355 restraints weight = 5978.316| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.05 r_work: 0.3084 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5966 Z= 0.102 Angle : 0.399 2.984 8037 Z= 0.228 Chirality : 0.043 0.142 895 Planarity : 0.002 0.016 1035 Dihedral : 4.488 16.267 810 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.66 % Allowed : 15.08 % Favored : 84.26 % 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: 1.20 (0.30), residues: 765 helix: 2.69 (0.67), residues: 70 sheet: 0.54 (0.31), residues: 280 loop : 0.82 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.011 0.001 PHE D 128 TYR 0.004 0.001 TYR F 83 ARG 0.001 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02009 ( 71) hydrogen bonds : angle 3.87570 ( 213) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.18908 ( 2) covalent geometry : bond 0.00223 ( 5965) covalent geometry : angle 0.39877 ( 8035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.681 Fit side-chains REVERT: C 5 GLU cc_start: 0.8151 (mp0) cc_final: 0.7599 (mp0) REVERT: C 17 LYS cc_start: 0.7935 (ttmt) cc_final: 0.6743 (ttpt) REVERT: C 114 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8671 (mmmt) REVERT: C 129 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: D 129 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8549 (tm-30) REVERT: E 17 LYS cc_start: 0.7868 (ttmt) cc_final: 0.6807 (ttpt) REVERT: E 129 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8442 (tp30) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 1.6897 time to fit residues: 188.7590 Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106141 restraints weight = 5905.099| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.06 r_work: 0.3000 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5966 Z= 0.210 Angle : 0.519 3.842 8037 Z= 0.289 Chirality : 0.045 0.153 895 Planarity : 0.003 0.019 1035 Dihedral : 5.098 19.832 810 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.15 % Allowed : 15.25 % Favored : 83.61 % 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: 1.12 (0.29), residues: 765 helix: 2.28 (0.64), residues: 70 sheet: 0.49 (0.31), residues: 280 loop : 0.83 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 75 HIS 0.004 0.002 HIS A 90 PHE 0.016 0.002 PHE C 128 TYR 0.007 0.002 TYR A 138 ARG 0.001 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 71) hydrogen bonds : angle 4.14843 ( 213) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.07798 ( 2) covalent geometry : bond 0.00471 ( 5965) covalent geometry : angle 0.51893 ( 8035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.728 Fit side-chains REVERT: A 62 VAL cc_start: 0.8580 (m) cc_final: 0.8330 (t) REVERT: C 5 GLU cc_start: 0.8143 (mp0) cc_final: 0.7584 (mp0) REVERT: C 17 LYS cc_start: 0.7972 (ttmt) cc_final: 0.6709 (ttpt) REVERT: C 114 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8847 (mmmt) REVERT: C 129 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: E 17 LYS cc_start: 0.8011 (ttmt) cc_final: 0.6827 (ttpt) REVERT: E 129 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: F 113 LYS cc_start: 0.8611 (mtmm) cc_final: 0.7954 (mptp) outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 1.7791 time to fit residues: 196.8106 Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113415 restraints weight = 5895.603| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.04 r_work: 0.3071 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5966 Z= 0.104 Angle : 0.404 3.220 8037 Z= 0.230 Chirality : 0.043 0.143 895 Planarity : 0.002 0.017 1035 Dihedral : 4.465 16.564 810 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 14.92 % Favored : 83.61 % 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: 1.29 (0.30), residues: 765 helix: 2.75 (0.67), residues: 70 sheet: 0.53 (0.31), residues: 280 loop : 0.93 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.010 0.001 PHE D 128 TYR 0.004 0.001 TYR A 83 ARG 0.001 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.01960 ( 71) hydrogen bonds : angle 3.96957 ( 213) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.12609 ( 2) covalent geometry : bond 0.00233 ( 5965) covalent geometry : angle 0.40388 ( 8035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.678 Fit side-chains REVERT: C 5 GLU cc_start: 0.8090 (mp0) cc_final: 0.7555 (mp0) REVERT: C 17 LYS cc_start: 0.7923 (ttmt) cc_final: 0.6719 (ttpt) REVERT: C 114 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8695 (mmmt) REVERT: C 129 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: E 17 LYS cc_start: 0.7879 (ttmt) cc_final: 0.6803 (ttpt) REVERT: E 129 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: F 113 LYS cc_start: 0.8536 (mtmm) cc_final: 0.7955 (mptp) outliers start: 9 outliers final: 6 residues processed: 107 average time/residue: 1.9979 time to fit residues: 220.6826 Evaluate side-chains 107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112381 restraints weight = 5842.385| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.03 r_work: 0.3052 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5966 Z= 0.124 Angle : 0.428 3.497 8037 Z= 0.244 Chirality : 0.043 0.146 895 Planarity : 0.002 0.017 1035 Dihedral : 4.550 17.431 810 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 15.41 % Favored : 82.95 % 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: 1.28 (0.30), residues: 765 helix: 2.68 (0.66), residues: 70 sheet: 0.48 (0.31), residues: 280 loop : 0.99 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 65 HIS 0.003 0.001 HIS F 90 PHE 0.011 0.001 PHE C 128 TYR 0.005 0.001 TYR F 83 ARG 0.001 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02234 ( 71) hydrogen bonds : angle 4.04829 ( 213) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.08174 ( 2) covalent geometry : bond 0.00277 ( 5965) covalent geometry : angle 0.42840 ( 8035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.694 Fit side-chains REVERT: C 5 GLU cc_start: 0.8076 (mp0) cc_final: 0.7560 (mp0) REVERT: C 17 LYS cc_start: 0.7931 (ttmt) cc_final: 0.6716 (ttpt) REVERT: C 114 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8723 (mmmt) REVERT: C 129 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: E 17 LYS cc_start: 0.7888 (ttmt) cc_final: 0.6809 (ttpt) REVERT: E 129 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: F 113 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7964 (mptp) outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 1.7592 time to fit residues: 190.9519 Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.121153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103036 restraints weight = 5938.301| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.19 r_work: 0.3002 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 5966 Z= 0.299 Angle : 0.612 4.644 8037 Z= 0.337 Chirality : 0.048 0.159 895 Planarity : 0.004 0.024 1035 Dihedral : 5.407 21.458 810 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 15.25 % Favored : 82.95 % 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: 0.95 (0.29), residues: 765 helix: 1.99 (0.61), residues: 70 sheet: 0.33 (0.30), residues: 290 loop : 0.80 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 75 HIS 0.006 0.003 HIS A 90 PHE 0.019 0.003 PHE C 128 TYR 0.011 0.003 TYR A 96 ARG 0.003 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 71) hydrogen bonds : angle 4.34384 ( 213) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.06444 ( 2) covalent geometry : bond 0.00676 ( 5965) covalent geometry : angle 0.61231 ( 8035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.039 Fit side-chains REVERT: A 62 VAL cc_start: 0.8595 (m) cc_final: 0.8378 (t) REVERT: C 5 GLU cc_start: 0.8083 (mp0) cc_final: 0.7539 (mp0) REVERT: C 17 LYS cc_start: 0.8019 (ttmt) cc_final: 0.6697 (ttpt) REVERT: C 114 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8824 (mmmt) REVERT: C 129 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: E 17 LYS cc_start: 0.8042 (ttmt) cc_final: 0.6776 (ttpt) REVERT: E 113 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8345 (mppt) REVERT: E 129 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: F 113 LYS cc_start: 0.8654 (mtmm) cc_final: 0.7898 (mptp) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 2.0269 time to fit residues: 232.7448 Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 0.0370 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113650 restraints weight = 5981.394| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.05 r_work: 0.3103 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5966 Z= 0.093 Angle : 0.397 3.171 8037 Z= 0.228 Chirality : 0.042 0.141 895 Planarity : 0.002 0.018 1035 Dihedral : 4.363 15.658 810 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.49 % Allowed : 16.56 % Favored : 82.95 % 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: 1.29 (0.30), residues: 765 helix: 2.75 (0.67), residues: 70 sheet: 0.51 (0.32), residues: 280 loop : 0.95 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.002 0.001 HIS F 90 PHE 0.010 0.001 PHE D 128 TYR 0.005 0.001 TYR A 83 ARG 0.001 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.01765 ( 71) hydrogen bonds : angle 4.01128 ( 213) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.13212 ( 2) covalent geometry : bond 0.00203 ( 5965) covalent geometry : angle 0.39668 ( 8035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.781 Fit side-chains REVERT: C 5 GLU cc_start: 0.8042 (mp0) cc_final: 0.7515 (mp0) REVERT: C 17 LYS cc_start: 0.7916 (ttmt) cc_final: 0.6702 (ttpt) REVERT: C 114 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8671 (mmmt) REVERT: C 129 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8319 (tp30) REVERT: E 17 LYS cc_start: 0.7882 (ttmt) cc_final: 0.6815 (ttpt) outliers start: 3 outliers final: 3 residues processed: 98 average time/residue: 2.3479 time to fit residues: 238.1112 Evaluate side-chains 100 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.128617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111817 restraints weight = 6039.439| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.06 r_work: 0.3078 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5966 Z= 0.121 Angle : 0.427 3.419 8037 Z= 0.244 Chirality : 0.043 0.146 895 Planarity : 0.003 0.019 1035 Dihedral : 4.473 16.727 810 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.66 % Allowed : 16.39 % Favored : 82.95 % 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: 1.31 (0.30), residues: 765 helix: 2.72 (0.66), residues: 70 sheet: 0.48 (0.31), residues: 280 loop : 1.01 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 65 HIS 0.003 0.001 HIS F 90 PHE 0.011 0.001 PHE C 128 TYR 0.006 0.001 TYR F 83 ARG 0.001 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.02149 ( 71) hydrogen bonds : angle 4.02208 ( 213) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.09299 ( 2) covalent geometry : bond 0.00267 ( 5965) covalent geometry : angle 0.42664 ( 8035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7510.66 seconds wall clock time: 131 minutes 55.65 seconds (7915.65 seconds total)