Starting phenix.real_space_refine on Fri Sep 11 13:53:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzw_30261/09_2026/7bzw_30261.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 36 5.16 5 C 6120 2.51 5 N 1656 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9756 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "3" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "4" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "5" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "7" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "8" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "9" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "10" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "11" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "12" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 2.05, per 1000 atoms: 0.21 Number of scatterers: 9756 At special positions: 0 Unit cell: (113.42, 114.48, 104.94, 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 36 16.00 O 1944 8.00 N 1656 7.00 C 6120 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: 0.89 Conformation dependent library (CDL) restraints added in 301.3 milliseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '1' and resid 130 through 133 Processing sheet with id=AA2, first strand: chain '1' and resid 152 through 155 Processing sheet with id=AA3, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AA4, first strand: chain '2' and resid 152 through 155 Processing sheet with id=AA5, first strand: chain '3' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain '3' and resid 152 through 155 Processing sheet with id=AA7, first strand: chain '4' and resid 130 through 133 Processing sheet with id=AA8, first strand: chain '4' and resid 152 through 155 Processing sheet with id=AA9, first strand: chain '5' and resid 130 through 133 Processing sheet with id=AB1, first strand: chain '5' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain '6' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain '6' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain '7' and resid 130 through 133 Processing sheet with id=AB5, first strand: chain '7' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain '8' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain '8' and resid 152 through 155 Processing sheet with id=AB8, first strand: chain '9' and resid 130 through 133 Processing sheet with id=AB9, first strand: chain '9' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain '10' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain '10' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain '11' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain '11' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain '12' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain '12' and resid 152 through 155 288 hydrogen bonds defined for protein. 720 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: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3252 1.34 - 1.46: 1639 1.46 - 1.58: 4937 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 9888 Sorted by residual: bond pdb=" CA GLY 4 165 " pdb=" C GLY 4 165 " ideal model delta sigma weight residual 1.516 1.509 0.007 1.01e-02 9.80e+03 4.95e-01 bond pdb=" N LYS11 216 " pdb=" CA LYS11 216 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.86e-01 bond pdb=" N GLY 6 165 " pdb=" CA GLY 6 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.84e-01 bond pdb=" N GLY12 165 " pdb=" CA GLY12 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.82e-01 bond pdb=" N GLY 7 165 " pdb=" CA GLY 7 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.74e-01 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 10934 0.92 - 1.85: 1741 1.85 - 2.77: 388 2.77 - 3.69: 113 3.69 - 4.61: 84 Bond angle restraints: 13260 Sorted by residual: angle pdb=" C ILE 6 131 " pdb=" N LYS 6 132 " pdb=" CA LYS 6 132 " ideal model delta sigma weight residual 121.63 117.02 4.61 1.92e+00 2.71e-01 5.78e+00 angle pdb=" C ILE 2 131 " pdb=" N LYS 2 132 " pdb=" CA LYS 2 132 " ideal model delta sigma weight residual 121.63 117.03 4.60 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C ILE 8 131 " pdb=" N LYS 8 132 " pdb=" CA LYS 8 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE10 131 " pdb=" N LYS10 132 " pdb=" CA LYS10 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE 7 131 " pdb=" N LYS 7 132 " pdb=" CA LYS 7 132 " ideal model delta sigma weight residual 121.63 117.05 4.58 1.92e+00 2.71e-01 5.69e+00 ... (remaining 13255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.42: 4716 11.42 - 22.84: 935 22.84 - 34.26: 469 34.26 - 45.67: 72 45.67 - 57.09: 60 Dihedral angle restraints: 6252 sinusoidal: 2736 harmonic: 3516 Sorted by residual: dihedral pdb=" CA GLU 9 195 " pdb=" C GLU 9 195 " pdb=" N LYS 9 196 " pdb=" CA LYS 9 196 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 4 195 " pdb=" C GLU 4 195 " pdb=" N LYS 4 196 " pdb=" CA LYS 4 196 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 5 195 " pdb=" C GLU 5 195 " pdb=" N LYS 5 196 " pdb=" CA LYS 5 196 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 650 0.028 - 0.056: 426 0.056 - 0.085: 229 0.085 - 0.113: 89 0.113 - 0.141: 82 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE 3 138 " pdb=" N ILE 3 138 " pdb=" C ILE 3 138 " pdb=" CB ILE 3 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE 8 138 " pdb=" N ILE 8 138 " pdb=" C ILE 8 138 " pdb=" CB ILE 8 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE 6 138 " pdb=" N ILE 6 138 " pdb=" C ILE 6 138 " pdb=" CB ILE 6 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1473 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 4 190 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO 4 191 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 4 191 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 191 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 2 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 2 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 2 191 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 5 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 5 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 5 191 " -0.029 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 740 2.72 - 3.27: 10669 3.27 - 3.81: 15449 3.81 - 4.36: 18051 4.36 - 4.90: 28123 Nonbonded interactions: 73032 Sorted by model distance: nonbonded pdb=" OE1 GLN 9 167 " pdb=" OH TYR 9 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 5 167 " pdb=" OH TYR 5 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 3 167 " pdb=" OH TYR 3 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN11 167 " pdb=" OH TYR11 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 4 167 " pdb=" OH TYR 4 184 " model vdw 2.176 3.040 ... (remaining 73027 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: 0.02 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain '10' selection = chain '11' selection = chain '12' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain '10' selection = chain '11' selection = chain '12' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9888 Z= 0.166 Angle : 0.823 4.614 13260 Z= 0.458 Chirality : 0.054 0.141 1476 Planarity : 0.006 0.053 1704 Dihedral : 15.818 57.093 3948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 28.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.36 % Favored : 80.64 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.20), residues: 1188 helix: -5.58 (0.06), residues: 72 sheet: -3.01 (0.21), residues: 420 loop : -4.13 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 187 TYR 0.009 0.003 TYR11 184 PHE 0.005 0.001 PHE 5 142 TRP 0.010 0.002 TRP10 129 HIS 0.001 0.000 HIS 4 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 9888) covalent geometry : angle 0.82273 / 0.46 (13260) hydrogen bonds : bond 0.03960 / 2.66 ( 288) hydrogen bonds : angle 8.28869 / 5.50 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 217 VAL cc_start: 0.8057 (t) cc_final: 0.7734 (p) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0739 time to fit residues: 2.5913 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.042890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033648 restraints weight = 10503.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.034381 restraints weight = 7945.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034911 restraints weight = 6506.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035315 restraints weight = 5613.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035638 restraints weight = 5016.338| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9888 Z= 0.161 Angle : 0.785 4.125 13260 Z= 0.418 Chirality : 0.054 0.168 1476 Planarity : 0.006 0.051 1704 Dihedral : 7.198 27.921 1260 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.21 % Favored : 78.79 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -2.21 (0.21), residues: 456 loop : -3.75 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 2 179 TYR 0.008 0.004 TYR 6 184 PHE 0.012 0.003 PHE 5 142 TRP 0.007 0.001 TRP 3 176 HIS 0.000 0.000 HIS 1 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9888) covalent geometry : angle 0.78463 / 0.42 (13260) hydrogen bonds : bond 0.02753 / 1.82 ( 288) hydrogen bonds : angle 7.64201 / 5.13 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 147 LEU cc_start: 0.8160 (tp) cc_final: 0.7898 (tp) REVERT: 9 196 LYS cc_start: 0.6770 (tttt) cc_final: 0.6501 (tptt) REVERT: 9 217 VAL cc_start: 0.8845 (t) cc_final: 0.8510 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0858 time to fit residues: 2.1911 Evaluate side-chains 15 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 9 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.040791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.031040 restraints weight = 10257.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031729 restraints weight = 7646.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.032212 restraints weight = 6275.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.032546 restraints weight = 5452.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.032713 restraints weight = 4946.373| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9888 Z= 0.138 Angle : 0.692 5.321 13260 Z= 0.372 Chirality : 0.053 0.199 1476 Planarity : 0.005 0.048 1704 Dihedral : 6.471 22.794 1260 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.66 (0.22), residues: 456 loop : -3.43 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG 2 141 TYR 0.008 0.003 TYR 5 184 PHE 0.011 0.003 PHE 7 142 TRP 0.009 0.001 TRP 9 176 HIS 0.000 0.000 HIS 1 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9888) covalent geometry : angle 0.69230 / 0.37 (13260) hydrogen bonds : bond 0.02691 / 1.73 ( 288) hydrogen bonds : angle 7.20829 / 4.86 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 131 ILE cc_start: 0.9499 (mm) cc_final: 0.9149 (mm) REVERT: 8 196 LYS cc_start: 0.7940 (tttt) cc_final: 0.7509 (mptt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0698 time to fit residues: 1.8529 Evaluate side-chains 19 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 91 optimal weight: 0.0040 overall best weight: 1.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.040206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030802 restraints weight = 10098.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.031446 restraints weight = 7677.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031916 restraints weight = 6334.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.032242 restraints weight = 5508.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032481 restraints weight = 4973.350| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9888 Z= 0.145 Angle : 0.710 5.315 13260 Z= 0.385 Chirality : 0.054 0.200 1476 Planarity : 0.005 0.049 1704 Dihedral : 6.916 21.958 1260 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.21), residues: 1188 helix: None (None), residues: 0 sheet: -1.28 (0.20), residues: 432 loop : -3.43 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 1 187 TYR 0.005 0.002 TYR 5 184 PHE 0.012 0.003 PHE 1 142 TRP 0.008 0.001 TRP 2 176 HIS 0.000 0.000 HIS11 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 9888) covalent geometry : angle 0.71022 / 0.39 (13260) hydrogen bonds : bond 0.02972 / 1.93 ( 288) hydrogen bonds : angle 6.59035 / 4.47 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 147 LEU cc_start: 0.6847 (tp) cc_final: 0.6267 (tp) REVERT: 8 196 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9068 (mptt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0661 time to fit residues: 1.5057 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 0.0370 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 0.0980 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 84 optimal weight: 0.0270 chunk 73 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.043155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.033042 restraints weight = 9539.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033933 restraints weight = 6900.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.034550 restraints weight = 5479.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035010 restraints weight = 4645.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035278 restraints weight = 4122.849| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9888 Z= 0.150 Angle : 0.702 4.560 13260 Z= 0.377 Chirality : 0.053 0.169 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.657 20.786 1260 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.69 (0.21), residues: 432 loop : -3.14 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 4 141 TYR 0.007 0.002 TYR 5 184 PHE 0.009 0.002 PHE 5 142 TRP 0.013 0.003 TRP10 129 HIS 0.002 0.001 HIS 7 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9888) covalent geometry : angle 0.70205 / 0.38 (13260) hydrogen bonds : bond 0.03043 / 1.97 ( 288) hydrogen bonds : angle 5.78302 / 3.91 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 147 LEU cc_start: 0.6925 (tp) cc_final: 0.6543 (tp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0714 time to fit residues: 1.5440 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 0.0170 chunk 48 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 68 optimal weight: 0.0030 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 0.0050 chunk 113 optimal weight: 0.0270 overall best weight: 0.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.042483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032461 restraints weight = 9668.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.033133 restraints weight = 7464.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.033629 restraints weight = 6214.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.033987 restraints weight = 5406.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034246 restraints weight = 4878.275| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9888 Z= 0.145 Angle : 0.734 4.818 13260 Z= 0.385 Chirality : 0.052 0.171 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.668 24.298 1260 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.25 (0.23), residues: 432 loop : -2.98 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 6 187 TYR 0.003 0.001 TYR 5 184 PHE 0.008 0.002 PHE 6 209 TRP 0.010 0.002 TRP 2 176 HIS 0.008 0.005 HIS12 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9888) covalent geometry : angle 0.73441 / 0.38 (13260) hydrogen bonds : bond 0.02944 / 1.91 ( 288) hydrogen bonds : angle 5.68876 / 3.85 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 196 LYS cc_start: 0.7848 (tptt) cc_final: 0.7617 (mptt) REVERT: 11 210 ILE cc_start: 0.9646 (mp) cc_final: 0.8832 (mp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0557 time to fit residues: 1.3427 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 4 optimal weight: 0.0370 chunk 54 optimal weight: 0.0270 chunk 56 optimal weight: 0.0980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 42 optimal weight: 10.0000 overall best weight: 0.0466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.043312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033529 restraints weight = 9687.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034327 restraints weight = 7014.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034922 restraints weight = 5658.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035325 restraints weight = 4836.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035653 restraints weight = 4329.774| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.7806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9888 Z= 0.157 Angle : 0.815 6.102 13260 Z= 0.418 Chirality : 0.053 0.151 1476 Planarity : 0.005 0.044 1704 Dihedral : 6.566 21.917 1260 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.24), residues: 1188 helix: None (None), residues: 0 sheet: -0.05 (0.23), residues: 432 loop : -2.43 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 5 141 TYR 0.008 0.002 TYR 5 184 PHE 0.009 0.003 PHE 5 209 TRP 0.013 0.003 TRP11 129 HIS 0.006 0.004 HIS 6 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9888) covalent geometry : angle 0.81508 / 0.42 (13260) hydrogen bonds : bond 0.03513 / 2.31 ( 288) hydrogen bonds : angle 5.62074 / 3.80 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 131 ILE cc_start: 0.9321 (mp) cc_final: 0.9107 (mm) REVERT: 11 196 LYS cc_start: 0.7557 (tptt) cc_final: 0.7310 (mptt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0525 time to fit residues: 1.2058 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 54 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.041443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031725 restraints weight = 9841.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.032353 restraints weight = 7453.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.032797 restraints weight = 6221.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.033101 restraints weight = 5506.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033266 restraints weight = 5072.957| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9888 Z= 0.157 Angle : 0.785 7.580 13260 Z= 0.410 Chirality : 0.055 0.168 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.567 19.495 1260 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.24), residues: 1188 helix: None (None), residues: 0 sheet: -0.00 (0.23), residues: 432 loop : -2.38 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 5 141 TYR 0.005 0.001 TYR 5 184 PHE 0.010 0.002 PHE 8 209 TRP 0.005 0.001 TRP 2 176 HIS 0.000 0.000 HIS 7 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 9888) covalent geometry : angle 0.78546 / 0.41 (13260) hydrogen bonds : bond 0.02770 / 1.78 ( 288) hydrogen bonds : angle 5.13532 / 3.49 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 196 LYS cc_start: 0.9048 (tppp) cc_final: 0.8785 (mptt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0575 time to fit residues: 1.1455 Evaluate side-chains 15 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 22 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.042002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032363 restraints weight = 9631.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033056 restraints weight = 7283.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.033555 restraints weight = 6034.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033852 restraints weight = 5300.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034098 restraints weight = 4880.358| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9888 Z= 0.146 Angle : 0.792 8.155 13260 Z= 0.409 Chirality : 0.054 0.171 1476 Planarity : 0.005 0.047 1704 Dihedral : 6.592 19.582 1260 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.24 (0.21), residues: 432 loop : -2.40 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 5 141 TYR 0.004 0.001 TYR 6 184 PHE 0.011 0.002 PHE 8 209 TRP 0.008 0.001 TRP 7 176 HIS 0.000 0.000 HIS 1 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9888) covalent geometry : angle 0.79186 / 0.41 (13260) hydrogen bonds : bond 0.03293 / 2.12 ( 288) hydrogen bonds : angle 4.85005 / 3.26 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 196 LYS cc_start: 0.8922 (tppp) cc_final: 0.8677 (mptt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0540 time to fit residues: 1.0784 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 0.0030 chunk 56 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 0.0970 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.0010 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.0060 overall best weight: 0.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.043566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.033464 restraints weight = 9517.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034172 restraints weight = 7311.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034695 restraints weight = 6097.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035062 restraints weight = 5348.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035341 restraints weight = 4843.050| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9888 Z= 0.158 Angle : 0.822 8.208 13260 Z= 0.418 Chirality : 0.054 0.173 1476 Planarity : 0.005 0.045 1704 Dihedral : 6.022 17.015 1260 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.26 (0.20), residues: 432 loop : -2.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 8 179 TYR 0.005 0.002 TYR 6 184 PHE 0.015 0.003 PHE 6 209 TRP 0.013 0.001 TRP 4 176 HIS 0.000 0.000 HIS12 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9888) covalent geometry : angle 0.82161 / 0.42 (13260) hydrogen bonds : bond 0.03557 / 2.31 ( 288) hydrogen bonds : angle 5.39503 / 3.66 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0463 time to fit residues: 0.8909 Evaluate side-chains 14 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 0.0070 chunk 82 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 0.0070 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 3.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.039753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.030242 restraints weight = 10267.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.030905 restraints weight = 7893.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031373 restraints weight = 6568.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.031696 restraints weight = 5731.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.031855 restraints weight = 5210.734| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9888 Z= 0.174 Angle : 0.736 4.840 13260 Z= 0.384 Chirality : 0.052 0.141 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.394 18.812 1260 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.38 (0.21), residues: 456 loop : -2.15 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG10 219 TYR 0.004 0.001 TYR 5 184 PHE 0.007 0.002 PHE 6 209 TRP 0.005 0.001 TRP 8 129 HIS 0.000 0.000 HIS12 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9888) covalent geometry : angle 0.73598 / 0.38 (13260) hydrogen bonds : bond 0.03532 / 2.35 ( 288) hydrogen bonds : angle 5.88580 / 3.94 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 986.31 seconds wall clock time: 18 minutes 4.54 seconds (1084.54 seconds total)