Starting phenix.real_space_refine on Tue Aug 4 21:22:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkg_48326/08_2026/9mkg_48326.cif" } resolution = 3.45 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= 0.048 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2688 2.51 5 N 721 2.21 5 O 837 1.98 5 H 2374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6636 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2297 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 2282 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 213, 2282 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2303 Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 2388 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 203} Chain: "C" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1951 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU A 148 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 148 " occ=0.43 residue: pdb=" N LEU B 96 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 96 " occ=0.00 Time building chain proxies: 1.57, per 1000 atoms: 0.24 Number of scatterers: 6636 At special positions: 0 Unit cell: (74.2416, 78.3661, 120.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 837 8.00 N 721 7.00 C 2688 6.00 H 2374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 84 " distance=2.03 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: 0.49 Conformation dependent library (CDL) restraints added in 227.7 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 15 sheets defined 8.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 153 through 158 removed outlier: 4.284A pdb=" N SER A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.769A pdb=" N HIS B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 92 through 96 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.820A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.667A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.868A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.264A pdb=" N TYR A 194 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.317A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 122 removed outlier: 3.877A pdb=" N ASN B 142 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR B 177 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 164 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 157 through 158 removed outlier: 3.569A pdb=" N LYS B 211 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AB6, first strand: chain 'C' and resid 20 through 22 165 hydrogen bonds defined for protein. 363 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: 1.25 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2374 1.03 - 1.23: 6 1.23 - 1.42: 1853 1.42 - 1.62: 2484 1.62 - 1.81: 21 Bond restraints: 6738 Sorted by residual: bond pdb=" N GLY B 72 " pdb=" CA GLY B 72 " ideal model delta sigma weight residual 1.460 1.449 0.011 1.26e-02 6.30e+03 8.03e-01 bond pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.33e-02 5.65e+03 5.10e-01 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.506 1.530 -0.024 3.90e-02 6.57e+02 3.82e-01 bond pdb=" CB TYR B 40 " pdb=" CG TYR B 40 " ideal model delta sigma weight residual 1.512 1.500 0.012 2.20e-02 2.07e+03 2.95e-01 bond pdb=" C TYR C 42 " pdb=" N TRP C 43 " ideal model delta sigma weight residual 1.331 1.324 0.007 1.44e-02 4.82e+03 2.64e-01 ... (remaining 6733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 10393 0.81 - 1.63: 849 1.63 - 2.44: 66 2.44 - 3.25: 21 3.25 - 4.07: 10 Bond angle restraints: 11339 Sorted by residual: angle pdb=" N LYS B 194 " pdb=" CA LYS B 194 " pdb=" C LYS B 194 " ideal model delta sigma weight residual 110.80 114.53 -3.73 2.13e+00 2.20e-01 3.07e+00 angle pdb=" N TYR C 33 " pdb=" CA TYR C 33 " pdb=" C TYR C 33 " ideal model delta sigma weight residual 113.18 111.35 1.83 1.21e+00 6.83e-01 2.30e+00 angle pdb=" CA LYS B 194 " pdb=" C LYS B 194 " pdb=" N VAL B 195 " ideal model delta sigma weight residual 116.84 119.16 -2.32 1.71e+00 3.42e-01 1.84e+00 angle pdb=" CA LYS B 194 " pdb=" C LYS B 194 " pdb=" O LYS B 194 " ideal model delta sigma weight residual 120.51 118.58 1.93 1.43e+00 4.89e-01 1.82e+00 angle pdb=" C MET A 48 " pdb=" N GLY A 49 " pdb=" CA GLY A 49 " ideal model delta sigma weight residual 121.22 118.58 2.64 2.07e+00 2.33e-01 1.62e+00 ... (remaining 11334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2986 17.80 - 35.60: 334 35.60 - 53.41: 92 53.41 - 71.21: 24 71.21 - 89.01: 13 Dihedral angle restraints: 3449 sinusoidal: 1687 harmonic: 1762 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 62.18 30.82 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 65.19 27.81 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA LEU B 140 " pdb=" C LEU B 140 " pdb=" N ASN B 141 " pdb=" CA ASN B 141 " ideal model delta harmonic sigma weight residual -180.00 -163.88 -16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 3446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 382 0.027 - 0.055: 180 0.055 - 0.082: 35 0.082 - 0.110: 51 0.110 - 0.137: 15 Chirality restraints: 663 Sorted by residual: chirality pdb=" CA ILE C 30 " pdb=" N ILE C 30 " pdb=" C ILE C 30 " pdb=" CB ILE C 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 79 " pdb=" N ILE B 79 " pdb=" C ILE B 79 " pdb=" CB ILE B 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 660 not shown) Planarity restraints: 1059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C AGLU A 148 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.20e-01 pdb=" N PRO A 149 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C BGLU A 148 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.12e-01 pdb=" N PRO A 149 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 122 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.26e-01 pdb=" N PRO B 123 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.012 5.00e-02 4.00e+02 ... (remaining 1056 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 581 2.23 - 2.83: 11019 2.83 - 3.42: 13775 3.42 - 4.01: 20018 4.01 - 4.60: 29881 Nonbonded interactions: 75274 Sorted by model distance: nonbonded pdb="HE21 GLN A 171 " pdb=" O LEU A 175 " model vdw 1.643 2.450 nonbonded pdb=" HZ1 LYS B 149 " pdb=" OE1 GLN B 151 " model vdw 1.669 2.450 nonbonded pdb=" OE1 GLN C 63 " pdb=" H GLU C 64 " model vdw 1.699 2.450 nonbonded pdb=" OE2 GLU C 104 " pdb=" HZ3 LYS C 109 " model vdw 1.716 2.450 nonbonded pdb=" OD1 ASP A 144 " pdb="HE22 GLN A 171 " model vdw 1.719 2.450 ... (remaining 75269 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 0.024 4369 Z= 0.121 Angle : 0.453 4.068 5948 Z= 0.238 Chirality : 0.043 0.137 663 Planarity : 0.003 0.024 767 Dihedral : 17.809 89.010 1573 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.41 % Allowed : 29.46 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.36), residues: 548 helix: 1.96 (1.28), residues: 15 sheet: -0.29 (0.33), residues: 247 loop : 0.07 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.011 0.001 TYR A 91 PHE 0.012 0.001 PHE A 100 TRP 0.008 0.001 TRP A 103 HIS 0.002 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4364) covalent geometry : angle 0.45288 / 0.24 ( 5938) SS BOND : bond 0.00181 / 0.10 ( 5) SS BOND : angle 0.46136 / 0.30 ( 10) hydrogen bonds : bond 0.13056 / 9.06 ( 150) hydrogen bonds : angle 6.73551 / 4.57 ( 363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1732 time to fit residues: 12.0064 Evaluate side-chains 59 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102497 restraints weight = 26367.440| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.80 r_work: 0.2892 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4369 Z= 0.208 Angle : 0.517 4.251 5948 Z= 0.272 Chirality : 0.045 0.145 663 Planarity : 0.003 0.027 767 Dihedral : 4.157 33.490 594 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.11 % Allowed : 28.63 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.37), residues: 548 helix: 1.81 (1.26), residues: 15 sheet: -0.28 (0.33), residues: 249 loop : -0.14 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.013 0.001 TYR A 91 PHE 0.016 0.001 PHE A 100 TRP 0.011 0.002 TRP A 103 HIS 0.003 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 4364) covalent geometry : angle 0.51685 / 0.27 ( 5938) SS BOND : bond 0.00345 / 0.18 ( 5) SS BOND : angle 0.73564 / 0.51 ( 10) hydrogen bonds : bond 0.03466 / 2.16 ( 150) hydrogen bonds : angle 5.56725 / 3.79 ( 363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 TRP cc_start: 0.7129 (OUTLIER) cc_final: 0.6600 (m-90) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.1132 time to fit residues: 10.1925 Evaluate side-chains 77 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104806 restraints weight = 24982.064| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.00 r_work: 0.2962 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4369 Z= 0.127 Angle : 0.453 4.111 5948 Z= 0.236 Chirality : 0.043 0.129 663 Planarity : 0.003 0.026 767 Dihedral : 3.938 31.701 594 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.32 % Allowed : 29.05 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.37), residues: 548 helix: 2.14 (1.31), residues: 15 sheet: -0.22 (0.33), residues: 249 loop : -0.03 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.009 0.001 TYR A 91 PHE 0.011 0.001 PHE A 100 TRP 0.008 0.001 TRP A 103 HIS 0.002 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4364) covalent geometry : angle 0.45248 / 0.24 ( 5938) SS BOND : bond 0.00232 / 0.13 ( 5) SS BOND : angle 0.60956 / 0.39 ( 10) hydrogen bonds : bond 0.02889 / 1.81 ( 150) hydrogen bonds : angle 5.08075 / 3.48 ( 363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6654 (m-90) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.1232 time to fit residues: 10.9437 Evaluate side-chains 78 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.0470 chunk 5 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109656 restraints weight = 18832.885| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.86 r_work: 0.3087 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4369 Z= 0.109 Angle : 0.435 4.076 5948 Z= 0.225 Chirality : 0.043 0.134 663 Planarity : 0.003 0.026 767 Dihedral : 3.785 30.386 594 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.36 % Allowed : 27.80 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.37), residues: 548 helix: 2.39 (1.34), residues: 15 sheet: -0.13 (0.34), residues: 249 loop : 0.05 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.009 0.001 TYR A 91 PHE 0.010 0.001 PHE A 100 TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 4364) covalent geometry : angle 0.43487 / 0.23 ( 5938) SS BOND : bond 0.00207 / 0.11 ( 5) SS BOND : angle 0.58001 / 0.37 ( 10) hydrogen bonds : bond 0.02610 / 1.63 ( 150) hydrogen bonds : angle 4.78060 / 3.28 ( 363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 TRP cc_start: 0.7070 (OUTLIER) cc_final: 0.6562 (m-90) outliers start: 20 outliers final: 15 residues processed: 79 average time/residue: 0.1023 time to fit residues: 10.2267 Evaluate side-chains 81 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 84 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109647 restraints weight = 19979.757| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.38 r_work: 0.3063 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4369 Z= 0.111 Angle : 0.433 4.041 5948 Z= 0.224 Chirality : 0.043 0.134 663 Planarity : 0.003 0.028 767 Dihedral : 3.758 30.314 594 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.15 % Allowed : 28.63 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.37), residues: 548 helix: 2.44 (1.34), residues: 15 sheet: -0.10 (0.34), residues: 249 loop : 0.07 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.009 0.001 TYR A 91 PHE 0.010 0.001 PHE A 100 TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4364) covalent geometry : angle 0.43276 / 0.22 ( 5938) SS BOND : bond 0.00206 / 0.11 ( 5) SS BOND : angle 0.56532 / 0.37 ( 10) hydrogen bonds : bond 0.02584 / 1.61 ( 150) hydrogen bonds : angle 4.70884 / 3.23 ( 363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.6551 (m-90) outliers start: 19 outliers final: 18 residues processed: 75 average time/residue: 0.1078 time to fit residues: 9.9917 Evaluate side-chains 82 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 84 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109161 restraints weight = 18446.704| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.85 r_work: 0.3061 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4369 Z= 0.125 Angle : 0.441 4.059 5948 Z= 0.228 Chirality : 0.043 0.134 663 Planarity : 0.003 0.028 767 Dihedral : 3.790 30.136 594 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.39 % Allowed : 27.59 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.37), residues: 548 helix: 2.45 (1.35), residues: 15 sheet: -0.14 (0.34), residues: 249 loop : 0.03 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 81 TYR 0.010 0.001 TYR A 91 PHE 0.011 0.001 PHE A 100 TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4364) covalent geometry : angle 0.44038 / 0.23 ( 5938) SS BOND : bond 0.00237 / 0.13 ( 5) SS BOND : angle 0.57683 / 0.38 ( 10) hydrogen bonds : bond 0.02639 / 1.64 ( 150) hydrogen bonds : angle 4.72885 / 3.24 ( 363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: C 5 TRP cc_start: 0.7061 (OUTLIER) cc_final: 0.6548 (m-90) outliers start: 25 outliers final: 22 residues processed: 80 average time/residue: 0.1035 time to fit residues: 10.3679 Evaluate side-chains 89 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105645 restraints weight = 24205.788| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.67 r_work: 0.3009 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4369 Z= 0.156 Angle : 0.464 4.113 5948 Z= 0.242 Chirality : 0.044 0.136 663 Planarity : 0.003 0.027 767 Dihedral : 3.940 30.306 594 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.81 % Allowed : 27.18 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.37), residues: 548 helix: 2.30 (1.33), residues: 15 sheet: -0.23 (0.34), residues: 249 loop : -0.07 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 81 TYR 0.011 0.001 TYR A 91 PHE 0.012 0.001 PHE A 100 TRP 0.007 0.001 TRP A 103 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 4364) covalent geometry : angle 0.46317 / 0.24 ( 5938) SS BOND : bond 0.00292 / 0.16 ( 5) SS BOND : angle 0.64388 / 0.44 ( 10) hydrogen bonds : bond 0.02826 / 1.75 ( 150) hydrogen bonds : angle 4.88215 / 3.34 ( 363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 5 TRP cc_start: 0.7115 (OUTLIER) cc_final: 0.6643 (m-90) outliers start: 27 outliers final: 24 residues processed: 84 average time/residue: 0.1033 time to fit residues: 10.7177 Evaluate side-chains 95 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 GLN B 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108178 restraints weight = 23058.444| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.59 r_work: 0.3015 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4369 Z= 0.120 Angle : 0.441 4.027 5948 Z= 0.229 Chirality : 0.043 0.134 663 Planarity : 0.003 0.027 767 Dihedral : 3.830 29.312 594 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.19 % Allowed : 27.80 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.37), residues: 548 helix: 2.42 (1.35), residues: 15 sheet: -0.20 (0.34), residues: 249 loop : -0.03 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 94 TYR 0.009 0.001 TYR A 91 PHE 0.010 0.001 PHE A 100 TRP 0.005 0.001 TRP A 103 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 4364) covalent geometry : angle 0.44078 / 0.23 ( 5938) SS BOND : bond 0.00236 / 0.13 ( 5) SS BOND : angle 0.62198 / 0.41 ( 10) hydrogen bonds : bond 0.02604 / 1.63 ( 150) hydrogen bonds : angle 4.73149 / 3.24 ( 363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 147 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 5 TRP cc_start: 0.7129 (OUTLIER) cc_final: 0.6633 (m-90) outliers start: 24 outliers final: 23 residues processed: 84 average time/residue: 0.0918 time to fit residues: 9.6461 Evaluate side-chains 91 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108089 restraints weight = 19042.130| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.93 r_work: 0.3053 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4369 Z= 0.139 Angle : 0.453 4.077 5948 Z= 0.235 Chirality : 0.043 0.134 663 Planarity : 0.003 0.027 767 Dihedral : 3.867 29.233 594 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.60 % Allowed : 27.59 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.37), residues: 548 helix: 2.34 (1.34), residues: 15 sheet: -0.21 (0.34), residues: 249 loop : -0.16 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.010 0.001 TYR A 91 PHE 0.012 0.001 PHE A 100 TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4364) covalent geometry : angle 0.45260 / 0.24 ( 5938) SS BOND : bond 0.00263 / 0.14 ( 5) SS BOND : angle 0.62561 / 0.42 ( 10) hydrogen bonds : bond 0.02719 / 1.69 ( 150) hydrogen bonds : angle 4.77478 / 3.26 ( 363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 147 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 5 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.6586 (m-90) outliers start: 26 outliers final: 25 residues processed: 87 average time/residue: 0.1313 time to fit residues: 13.8219 Evaluate side-chains 95 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111294 restraints weight = 17614.462| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.81 r_work: 0.3126 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4369 Z= 0.078 Angle : 0.414 3.925 5948 Z= 0.213 Chirality : 0.042 0.132 663 Planarity : 0.003 0.026 767 Dihedral : 3.593 27.304 594 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.11 % Allowed : 30.08 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.37), residues: 548 helix: 2.65 (1.40), residues: 15 sheet: -0.04 (0.34), residues: 249 loop : -0.00 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 93 TYR 0.006 0.001 TYR A 91 PHE 0.008 0.001 PHE A 100 TRP 0.005 0.001 TRP A 154 HIS 0.001 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 ( 4364) covalent geometry : angle 0.41331 / 0.21 ( 5938) SS BOND : bond 0.00172 / 0.09 ( 5) SS BOND : angle 0.56529 / 0.37 ( 10) hydrogen bonds : bond 0.02297 / 1.45 ( 150) hydrogen bonds : angle 4.42965 / 3.04 ( 363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 147 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 5 TRP cc_start: 0.6984 (OUTLIER) cc_final: 0.6523 (m-90) outliers start: 14 outliers final: 13 residues processed: 74 average time/residue: 0.1390 time to fit residues: 12.4010 Evaluate side-chains 81 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107840 restraints weight = 22134.713| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.43 r_work: 0.3016 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4369 Z= 0.164 Angle : 0.465 4.129 5948 Z= 0.242 Chirality : 0.044 0.135 663 Planarity : 0.003 0.028 767 Dihedral : 3.857 28.969 594 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.73 % Allowed : 29.25 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.37), residues: 548 helix: 2.14 (1.27), residues: 15 sheet: -0.16 (0.34), residues: 249 loop : -0.17 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.012 0.001 TYR A 91 PHE 0.012 0.001 PHE A 100 TRP 0.007 0.001 TRP A 103 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 4364) covalent geometry : angle 0.46504 / 0.24 ( 5938) SS BOND : bond 0.00282 / 0.15 ( 5) SS BOND : angle 0.65538 / 0.44 ( 10) hydrogen bonds : bond 0.02816 / 1.73 ( 150) hydrogen bonds : angle 4.74160 / 3.24 ( 363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.84 seconds wall clock time: 27 minutes 20.59 seconds (1640.59 seconds total)