Starting phenix.real_space_refine on Wed Mar 4 00:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzw_30261/03_2026/7bzw_30261.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzw_30261/03_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_30261/03_2026/7bzw_30261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzw_30261/03_2026/7bzw_30261.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzw_30261/03_2026/7bzw_30261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzw_30261/03_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-dev-5986/lib/python3.9/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: 2.04, 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: 0.84 Conformation dependent library (CDL) restraints added in 274.9 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: 0.30 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: 1.31 Time building geometry restraints manager: 1.12 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: 0.03 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: 0.830 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 covalent geometry : bond 0.00342 ( 9888) covalent geometry : angle 0.82273 (13260) hydrogen bonds : bond 0.03960 ( 288) hydrogen bonds : angle 8.28869 ( 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: 0.0713 time to fit residues: 2.4844 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=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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3204 r_free = 0.3204 target = 0.042883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033645 restraints weight = 10508.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.034373 restraints weight = 7945.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034915 restraints weight = 6517.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035321 restraints weight = 5615.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035644 restraints weight = 5007.571| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4381 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 : 23.90 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 covalent geometry : bond 0.00367 ( 9888) covalent geometry : angle 0.78463 (13260) hydrogen bonds : bond 0.02753 ( 288) hydrogen bonds : angle 7.64201 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 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 : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 147 LEU cc_start: 0.8162 (tp) cc_final: 0.7902 (tp) REVERT: 9 196 LYS cc_start: 0.6771 (tttt) cc_final: 0.6501 (tptt) REVERT: 9 217 VAL cc_start: 0.8845 (t) cc_final: 0.8509 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0841 time to fit residues: 2.1563 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.040763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.031043 restraints weight = 10261.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031734 restraints weight = 7614.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.032211 restraints weight = 6241.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.032538 restraints weight = 5433.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.032775 restraints weight = 4924.731| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9888 Z= 0.136 Angle : 0.690 5.427 13260 Z= 0.371 Chirality : 0.053 0.201 1476 Planarity : 0.005 0.048 1704 Dihedral : 6.440 22.781 1260 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % 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: -3.95 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.68 (0.22), residues: 456 loop : -3.45 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 8 179 TYR 0.006 0.002 TYR12 184 PHE 0.012 0.003 PHE 3 142 TRP 0.008 0.001 TRP 9 176 HIS 0.000 0.000 HIS 7 136 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9888) covalent geometry : angle 0.69041 (13260) hydrogen bonds : bond 0.02699 ( 288) hydrogen bonds : angle 7.22294 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 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 : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 131 ILE cc_start: 0.9498 (mm) cc_final: 0.9165 (mm) REVERT: 8 147 LEU cc_start: 0.8110 (tp) cc_final: 0.7737 (tp) REVERT: 8 196 LYS cc_start: 0.7936 (tttt) cc_final: 0.7508 (mptt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0716 time to fit residues: 1.9012 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 : 0.021 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 44 optimal weight: 0.0050 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 91 optimal weight: 10.0000 overall best weight: 1.1010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.031112 restraints weight = 9864.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.031780 restraints weight = 7344.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.032228 restraints weight = 5994.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.032560 restraints weight = 5197.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.032763 restraints weight = 4694.261| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9888 Z= 0.141 Angle : 0.693 5.280 13260 Z= 0.376 Chirality : 0.054 0.201 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.654 22.377 1260 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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: -3.72 (0.21), residues: 1188 helix: None (None), residues: 0 sheet: -1.28 (0.21), residues: 432 loop : -3.43 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG12 187 TYR 0.005 0.002 TYR 6 184 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 covalent geometry : bond 0.00336 ( 9888) covalent geometry : angle 0.69283 (13260) hydrogen bonds : bond 0.02758 ( 288) hydrogen bonds : angle 6.54463 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 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: symmetry clash revert: symmetry clash REVERT: 8 223 ASP cc_start: 0.6695 (t0) cc_final: 0.6463 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0733 time to fit residues: 1.7407 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 : 0.034 ------------------------------------------------------------------------------- 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: 0.0770 chunk 81 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 0.0770 chunk 63 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 118 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.042076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.032244 restraints weight = 9655.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.032925 restraints weight = 7184.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.033411 restraints weight = 5862.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033764 restraints weight = 5068.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.034019 restraints weight = 4571.951| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.6183 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= 0.139 Angle : 0.690 3.920 13260 Z= 0.369 Chirality : 0.052 0.167 1476 Planarity : 0.005 0.047 1704 Dihedral : 6.511 20.608 1260 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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: -3.33 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.82 (0.21), residues: 432 loop : -3.29 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 6 187 TYR 0.005 0.002 TYR10 184 PHE 0.010 0.002 PHE 9 142 TRP 0.011 0.002 TRP10 129 HIS 0.002 0.001 HIS11 136 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9888) covalent geometry : angle 0.69041 (13260) hydrogen bonds : bond 0.02833 ( 288) hydrogen bonds : angle 5.85899 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 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 : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0704 time to fit residues: 1.5307 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 : 0.021 ------------------------------------------------------------------------------- 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: 8.9990 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 0.0870 chunk 37 optimal weight: 0.0370 chunk 27 optimal weight: 0.0000 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 0.0000 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 113 optimal weight: 0.1980 overall best weight: 0.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3231 r_free = 0.3231 target = 0.042031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.032666 restraints weight = 10226.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.033346 restraints weight = 7643.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033830 restraints weight = 6247.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.034133 restraints weight = 5424.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034352 restraints weight = 4965.224| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9888 Z= 0.135 Angle : 0.696 4.666 13260 Z= 0.366 Chirality : 0.051 0.154 1476 Planarity : 0.005 0.043 1704 Dihedral : 6.051 18.920 1260 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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: -2.83 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.43 (0.22), residues: 492 loop : -3.18 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 3 141 TYR 0.006 0.002 TYR 7 184 PHE 0.009 0.003 PHE 6 209 TRP 0.011 0.002 TRP 6 176 HIS 0.008 0.005 HIS 4 136 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9888) covalent geometry : angle 0.69628 (13260) hydrogen bonds : bond 0.03190 ( 288) hydrogen bonds : angle 5.50008 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 11 223 ASP cc_start: 0.7074 (t0) cc_final: 0.6820 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0551 time to fit residues: 1.3950 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 8 optimal weight: 0.0270 chunk 87 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3207 r_free = 0.3207 target = 0.041895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032458 restraints weight = 10078.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033130 restraints weight = 7566.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.033609 restraints weight = 6249.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033923 restraints weight = 5466.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.034089 restraints weight = 4971.037| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9888 Z= 0.143 Angle : 0.741 4.859 13260 Z= 0.381 Chirality : 0.052 0.145 1476 Planarity : 0.005 0.043 1704 Dihedral : 5.906 16.064 1260 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.30 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: -2.41 (0.25), residues: 1188 helix: None (None), residues: 0 sheet: -0.21 (0.23), residues: 492 loop : -2.82 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 1 179 TYR 0.005 0.002 TYR10 184 PHE 0.010 0.003 PHE10 209 TRP 0.010 0.001 TRP11 176 HIS 0.001 0.001 HIS 4 136 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9888) covalent geometry : angle 0.74134 (13260) hydrogen bonds : bond 0.02969 ( 288) hydrogen bonds : angle 5.30254 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 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 : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0488 time to fit residues: 1.2221 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 : 0.037 ------------------------------------------------------------------------------- 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: 0.5980 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.040103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030840 restraints weight = 10035.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031457 restraints weight = 7559.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031863 restraints weight = 6262.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032065 restraints weight = 5524.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032312 restraints weight = 5129.477| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9888 Z= 0.164 Angle : 0.840 7.936 13260 Z= 0.439 Chirality : 0.056 0.206 1476 Planarity : 0.005 0.045 1704 Dihedral : 6.157 19.585 1260 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % 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: -2.80 (0.24), residues: 1188 helix: None (None), residues: 0 sheet: -0.48 (0.23), residues: 492 loop : -3.08 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 4 141 TYR 0.004 0.002 TYR10 184 PHE 0.032 0.006 PHE 2 142 TRP 0.007 0.002 TRP 4 176 HIS 0.001 0.000 HIS 4 136 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9888) covalent geometry : angle 0.84049 (13260) hydrogen bonds : bond 0.03083 ( 288) hydrogen bonds : angle 5.49147 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 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 : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 11 222 ILE cc_start: 0.6784 (pt) cc_final: 0.6233 (mm) REVERT: 11 223 ASP cc_start: 0.7315 (t0) cc_final: 0.6933 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0539 time to fit residues: 1.2222 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 : 0.041 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.0050 chunk 22 optimal weight: 0.3980 chunk 59 optimal weight: 0.0370 chunk 13 optimal weight: 0.0970 chunk 98 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.041796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032611 restraints weight = 10033.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.033320 restraints weight = 7438.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033799 restraints weight = 6091.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034144 restraints weight = 5328.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.034379 restraints weight = 4838.210| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 9888 Z= 0.142 Angle : 0.732 5.449 13260 Z= 0.377 Chirality : 0.053 0.171 1476 Planarity : 0.005 0.045 1704 Dihedral : 5.864 19.192 1260 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % 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: -2.61 (0.24), residues: 1188 helix: None (None), residues: 0 sheet: -0.28 (0.23), residues: 492 loop : -3.02 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 1 141 TYR 0.003 0.002 TYR10 184 PHE 0.011 0.003 PHE 4 209 TRP 0.009 0.001 TRP 2 176 HIS 0.000 0.000 HIS 4 136 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9888) covalent geometry : angle 0.73240 (13260) hydrogen bonds : bond 0.03223 ( 288) hydrogen bonds : angle 5.03450 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0493 time to fit residues: 1.0644 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 : 0.037 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.041364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032260 restraints weight = 10006.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032856 restraints weight = 7588.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033252 restraints weight = 6297.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033564 restraints weight = 5599.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.033752 restraints weight = 5130.891| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9888 Z= 0.134 Angle : 0.709 4.973 13260 Z= 0.370 Chirality : 0.053 0.168 1476 Planarity : 0.005 0.044 1704 Dihedral : 5.851 19.314 1260 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 15.51 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: -2.99 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.66 (0.22), residues: 492 loop : -3.17 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG11 141 TYR 0.005 0.001 TYR 7 184 PHE 0.011 0.003 PHE 7 209 TRP 0.008 0.001 TRP 3 176 HIS 0.000 0.000 HIS 4 136 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9888) covalent geometry : angle 0.70917 (13260) hydrogen bonds : bond 0.03048 ( 288) hydrogen bonds : angle 5.07246 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.038 Fit side-chains revert: symmetry clash REVERT: 11 147 LEU cc_start: 0.8598 (tp) cc_final: 0.7560 (tp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0518 time to fit residues: 1.1055 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 : 0.035 ------------------------------------------------------------------------------- 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: 0.8980 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 0.0170 overall best weight: 0.9232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.041744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032339 restraints weight = 9253.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032997 restraints weight = 7042.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033435 restraints weight = 5880.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.033758 restraints weight = 5189.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033933 restraints weight = 4744.494| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.8448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9888 Z= 0.145 Angle : 0.811 6.365 13260 Z= 0.413 Chirality : 0.055 0.197 1476 Planarity : 0.005 0.044 1704 Dihedral : 6.116 18.650 1260 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -2.76 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.54 (0.22), residues: 492 loop : -2.99 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 8 141 TYR 0.002 0.001 TYR 3 184 PHE 0.026 0.005 PHE10 142 TRP 0.010 0.002 TRP 6 176 HIS 0.000 0.000 HIS12 136 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9888) covalent geometry : angle 0.81057 (13260) hydrogen bonds : bond 0.03259 ( 288) hydrogen bonds : angle 5.05605 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 982.29 seconds wall clock time: 18 minutes 7.55 seconds (1087.55 seconds total)