Starting phenix.real_space_refine on Tue Aug 4 14:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2026/9edc_47944.map" } resolution = 4.18 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= 0.049 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 P 6 5.49 5 S 12 5.16 5 C 2596 2.51 5 N 690 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4062 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2777 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2761 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 338, 2762 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 2816 Chain: "B" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.32 Number of scatterers: 4062 At special positions: 0 Unit cell: (73.632, 79.296, 85.904, 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 12 16.00 P 6 15.00 O 758 8.00 N 690 7.00 C 2596 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: 0.21 Conformation dependent library (CDL) restraints added in 226.9 milliseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 42.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.835A pdb=" N TYR A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 184 through 188 removed outlier: 4.643A pdb=" N PHE A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.020A pdb=" N TRP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.521A pdb=" N AGLY A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.207A pdb=" N ILE A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.290A pdb=" N THR A 299 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.463A pdb=" N HIS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.500A pdb=" N ILE B 204 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 51 removed outlier: 5.588A pdb=" N ARG A 45 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 61 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 47 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 57 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 121 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 106 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.661A pdb=" N LYS B 220 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.667A pdb=" N VAL B 213 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 184 " --> pdb=" O TRP B 188 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 471 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: 0.54 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 723 1.33 - 1.45: 1093 1.45 - 1.57: 2306 1.57 - 1.69: 16 1.69 - 1.81: 22 Bond restraints: 4160 Sorted by residual: bond pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" O3P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O2P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C PRO B 84 " pdb=" N PRO B 85 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.27e+00 bond pdb=" O1P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 5528 2.71 - 5.43: 87 5.43 - 8.14: 14 8.14 - 10.85: 2 10.85 - 13.57: 2 Bond angle restraints: 5633 Sorted by residual: angle pdb=" C PRO B 85 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " ideal model delta sigma weight residual 121.80 133.13 -11.33 2.44e+00 1.68e-01 2.16e+01 angle pdb=" C THR A 32 " pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta sigma weight residual 110.17 115.24 -5.07 1.11e+00 8.12e-01 2.09e+01 angle pdb=" CB TPO A 197 " pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 119.31 105.74 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N GLN A 96 " pdb=" CA GLN A 96 " pdb=" CB GLN A 96 " ideal model delta sigma weight residual 110.41 117.70 -7.29 1.68e+00 3.54e-01 1.88e+01 angle pdb=" C LEU A 95 " pdb=" N GLN A 96 " pdb=" CA GLN A 96 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 ... (remaining 5628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2264 17.88 - 35.76: 188 35.76 - 53.64: 29 53.64 - 71.52: 8 71.52 - 89.40: 4 Dihedral angle restraints: 2493 sinusoidal: 1038 harmonic: 1455 Sorted by residual: dihedral pdb=" CA LYS B 90 " pdb=" C LYS B 90 " pdb=" N GLY B 91 " pdb=" CA GLY B 91 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA THR A 195 " pdb=" C THR A 195 " pdb=" N TRP A 196 " pdb=" CA TRP A 196 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 201 " pdb=" C THR A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 444 0.052 - 0.104: 118 0.104 - 0.156: 33 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 599 Sorted by residual: chirality pdb=" CB THR A 32 " pdb=" CA THR A 32 " pdb=" OG1 THR A 32 " pdb=" CG2 THR A 32 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR A 32 " pdb=" N THR A 32 " pdb=" C THR A 32 " pdb=" CB THR A 32 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 596 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 32 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 33 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 168 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 169 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 119 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C VAL A 119 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 119 " 0.010 2.00e-02 2.50e+03 pdb=" N MET A 120 " 0.009 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 959 2.79 - 3.32: 3520 3.32 - 3.85: 7147 3.85 - 4.37: 8165 4.37 - 4.90: 13864 Nonbonded interactions: 33655 Sorted by model distance: nonbonded pdb=" OH TYR A 229 " pdb=" O ARG A 256 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" O VAL A 310 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 195 " pdb=" O2P TPO A 197 " model vdw 2.340 3.040 nonbonded pdb=" O PHE A 43 " pdb=" NH1 ARG A 45 " model vdw 2.409 3.120 nonbonded pdb=" NZ LYS A 111 " pdb=" O PHE A 347 " model vdw 2.410 3.120 ... (remaining 33650 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 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: 0.380 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5383 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 : 0.005 0.110 4160 Z= 0.245 Angle : 0.883 13.568 5633 Z= 0.482 Chirality : 0.051 0.260 599 Planarity : 0.006 0.065 718 Dihedral : 13.866 89.398 1559 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % 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 : 0.21 % 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: -1.43 (0.34), residues: 490 helix: -1.05 (0.33), residues: 192 sheet: -0.34 (0.59), residues: 66 loop : -0.91 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.019 0.002 TYR B 229 PHE 0.020 0.002 PHE A 145 TRP 0.021 0.002 TRP A 30 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.25 ( 4160) covalent geometry : angle 0.88266 / 0.48 ( 5633) hydrogen bonds : bond 0.16350 / 9.01 ( 169) hydrogen bonds : angle 6.50241 / 4.37 ( 471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6897 (mt) cc_final: 0.6544 (mt) REVERT: A 102 PHE cc_start: 0.9345 (m-80) cc_final: 0.8887 (m-80) REVERT: A 155 GLU cc_start: 0.9257 (tt0) cc_final: 0.8988 (tt0) REVERT: A 179 TYR cc_start: 0.1788 (m-80) cc_final: 0.1450 (m-80) REVERT: A 182 VAL cc_start: 0.9223 (t) cc_final: 0.8916 (p) REVERT: A 221 TRP cc_start: 0.9055 (m100) cc_final: 0.8368 (m100) REVERT: A 222 TRP cc_start: 0.9095 (t-100) cc_final: 0.8763 (t-100) REVERT: A 231 MET cc_start: 0.9110 (mtm) cc_final: 0.8721 (mmm) REVERT: A 236 PRO cc_start: 0.8786 (Cg_endo) cc_final: 0.7453 (Cg_exo) REVERT: A 301 ASP cc_start: 0.7956 (t0) cc_final: 0.7566 (p0) REVERT: A 308 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7859 (mtt90) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1063 time to fit residues: 18.9851 Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.3844 > 50:) chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 158 HIS B 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.138168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.084095 restraints weight = 28472.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.091215 restraints weight = 15681.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.096316 restraints weight = 10679.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.100334 restraints weight = 8098.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.103226 restraints weight = 6554.107| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 4160 Z= 0.276 Angle : 0.833 13.305 5633 Z= 0.428 Chirality : 0.048 0.172 599 Planarity : 0.006 0.062 718 Dihedral : 8.771 79.238 590 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.06 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -0.97 (0.36), residues: 490 helix: -0.73 (0.34), residues: 200 sheet: 0.89 (0.75), residues: 43 loop : -0.75 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 230 TYR 0.021 0.003 TYR A 247 PHE 0.033 0.003 PHE A 129 TRP 0.032 0.003 TRP A 30 HIS 0.008 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.28 ( 4160) covalent geometry : angle 0.83303 / 0.43 ( 5633) hydrogen bonds : bond 0.04923 / 3.23 ( 169) hydrogen bonds : angle 5.85089 / 3.96 ( 471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6802 (mt) cc_final: 0.6531 (mt) REVERT: A 155 GLU cc_start: 0.9222 (tt0) cc_final: 0.9001 (tt0) REVERT: A 167 LEU cc_start: 0.9067 (tp) cc_final: 0.8764 (tp) REVERT: A 216 ASN cc_start: 0.8955 (p0) cc_final: 0.8595 (p0) REVERT: A 221 TRP cc_start: 0.9002 (m100) cc_final: 0.8343 (m100) REVERT: A 222 TRP cc_start: 0.9261 (t-100) cc_final: 0.8645 (t-100) REVERT: A 301 ASP cc_start: 0.7974 (t0) cc_final: 0.7767 (p0) REVERT: A 324 THR cc_start: 0.8192 (t) cc_final: 0.7958 (m) REVERT: B 172 PHE cc_start: 0.9239 (t80) cc_final: 0.8792 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0695 time to fit residues: 9.3872 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.142901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.086370 restraints weight = 30694.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.094210 restraints weight = 15243.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.099843 restraints weight = 10019.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.104228 restraints weight = 7456.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.107372 restraints weight = 5980.678| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4160 Z= 0.142 Angle : 0.665 8.375 5633 Z= 0.349 Chirality : 0.046 0.198 599 Planarity : 0.005 0.058 718 Dihedral : 8.350 83.127 590 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.86 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.64 (0.36), residues: 490 helix: -0.32 (0.34), residues: 200 sheet: 0.68 (0.73), residues: 43 loop : -0.62 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 231 TYR 0.039 0.002 TYR A 247 PHE 0.024 0.002 PHE A 129 TRP 0.037 0.002 TRP A 302 HIS 0.009 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4160) covalent geometry : angle 0.66538 / 0.35 ( 5633) hydrogen bonds : bond 0.03810 / 2.42 ( 169) hydrogen bonds : angle 5.35336 / 3.66 ( 471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7137 (mt) cc_final: 0.6898 (mt) REVERT: A 102 PHE cc_start: 0.8588 (m-80) cc_final: 0.8069 (m-80) REVERT: A 155 GLU cc_start: 0.8894 (tt0) cc_final: 0.8666 (tt0) REVERT: A 205 LEU cc_start: 0.8035 (mm) cc_final: 0.7820 (mm) REVERT: A 216 ASN cc_start: 0.8323 (p0) cc_final: 0.8123 (m-40) REVERT: A 217 LYS cc_start: 0.8726 (mppt) cc_final: 0.8468 (mptt) REVERT: A 221 TRP cc_start: 0.8335 (m100) cc_final: 0.7895 (m100) REVERT: A 222 TRP cc_start: 0.8659 (t-100) cc_final: 0.8317 (t-100) REVERT: A 231 MET cc_start: 0.8774 (mtm) cc_final: 0.8064 (mtp) REVERT: A 301 ASP cc_start: 0.8279 (t0) cc_final: 0.8010 (p0) REVERT: A 324 THR cc_start: 0.8087 (t) cc_final: 0.7881 (m) REVERT: B 172 PHE cc_start: 0.9112 (t80) cc_final: 0.8466 (t80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0956 time to fit residues: 11.7151 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 2 optimal weight: 0.0010 chunk 12 optimal weight: 5.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.145545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.089990 restraints weight = 26602.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.097599 restraints weight = 13785.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.103493 restraints weight = 9173.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.107749 restraints weight = 6885.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.110820 restraints weight = 5540.522| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4160 Z= 0.119 Angle : 0.620 7.574 5633 Z= 0.323 Chirality : 0.044 0.159 599 Planarity : 0.005 0.061 718 Dihedral : 8.134 85.786 590 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.27 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.31 (0.37), residues: 490 helix: 0.08 (0.35), residues: 199 sheet: 0.62 (0.70), residues: 43 loop : -0.49 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 209 TYR 0.020 0.002 TYR A 247 PHE 0.013 0.001 PHE A 129 TRP 0.026 0.002 TRP A 302 HIS 0.008 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4160) covalent geometry : angle 0.61996 / 0.32 ( 5633) hydrogen bonds : bond 0.03467 / 2.26 ( 169) hydrogen bonds : angle 5.12548 / 3.45 ( 471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7075 (mt) cc_final: 0.6832 (mt) REVERT: A 102 PHE cc_start: 0.8525 (m-80) cc_final: 0.8074 (m-80) REVERT: A 155 GLU cc_start: 0.8813 (tt0) cc_final: 0.8570 (tt0) REVERT: A 217 LYS cc_start: 0.8780 (mppt) cc_final: 0.8199 (mmtm) REVERT: A 221 TRP cc_start: 0.8281 (m100) cc_final: 0.7869 (m100) REVERT: A 222 TRP cc_start: 0.8597 (t-100) cc_final: 0.8367 (t-100) REVERT: A 301 ASP cc_start: 0.8306 (t0) cc_final: 0.8033 (p0) REVERT: B 172 PHE cc_start: 0.9215 (t80) cc_final: 0.8416 (t80) REVERT: B 234 MET cc_start: 0.4030 (ptt) cc_final: 0.3705 (ptt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0939 time to fit residues: 11.0528 Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 2 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.146701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.085657 restraints weight = 35458.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.093896 restraints weight = 16703.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.099777 restraints weight = 10798.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.104268 restraints weight = 8052.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.107680 restraints weight = 6432.639| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4160 Z= 0.122 Angle : 0.634 9.994 5633 Z= 0.327 Chirality : 0.044 0.157 599 Planarity : 0.005 0.064 718 Dihedral : 7.972 84.214 590 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.27 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.37), residues: 490 helix: 0.44 (0.36), residues: 193 sheet: 0.38 (0.69), residues: 53 loop : -0.42 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 209 TYR 0.034 0.002 TYR A 247 PHE 0.028 0.001 PHE A 238 TRP 0.020 0.001 TRP A 302 HIS 0.007 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4160) covalent geometry : angle 0.63420 / 0.33 ( 5633) hydrogen bonds : bond 0.03493 / 2.27 ( 169) hydrogen bonds : angle 5.08489 / 3.46 ( 471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6632 (mt) cc_final: 0.6289 (mt) REVERT: A 102 PHE cc_start: 0.8725 (m-80) cc_final: 0.8248 (m-80) REVERT: A 120 MET cc_start: 0.9344 (tpt) cc_final: 0.9029 (tpp) REVERT: A 155 GLU cc_start: 0.9010 (tt0) cc_final: 0.8788 (tt0) REVERT: A 182 VAL cc_start: 0.9242 (p) cc_final: 0.9029 (p) REVERT: A 183 THR cc_start: 0.8672 (t) cc_final: 0.8168 (t) REVERT: A 216 ASN cc_start: 0.8192 (t0) cc_final: 0.7582 (m-40) REVERT: A 221 TRP cc_start: 0.8868 (m100) cc_final: 0.8223 (m100) REVERT: A 222 TRP cc_start: 0.8949 (t-100) cc_final: 0.8666 (t-100) REVERT: A 270 ARG cc_start: 0.8601 (mpt-90) cc_final: 0.8280 (mmt90) REVERT: A 301 ASP cc_start: 0.8307 (t0) cc_final: 0.8022 (p0) REVERT: B 172 PHE cc_start: 0.9377 (t80) cc_final: 0.8685 (t80) REVERT: B 234 MET cc_start: 0.4082 (ptt) cc_final: 0.2717 (ptt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0988 time to fit residues: 11.7385 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.141823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.082671 restraints weight = 31981.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.090071 restraints weight = 16431.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.095498 restraints weight = 10957.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.099655 restraints weight = 8276.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.102873 restraints weight = 6709.762| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4160 Z= 0.146 Angle : 0.633 7.455 5633 Z= 0.325 Chirality : 0.044 0.152 599 Planarity : 0.005 0.065 718 Dihedral : 7.952 80.743 590 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -0.05 (0.38), residues: 490 helix: 0.37 (0.36), residues: 199 sheet: 0.80 (0.76), residues: 43 loop : -0.43 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 209 TYR 0.019 0.002 TYR A 247 PHE 0.032 0.002 PHE A 238 TRP 0.017 0.002 TRP A 302 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 4160) covalent geometry : angle 0.63346 / 0.33 ( 5633) hydrogen bonds : bond 0.03470 / 2.31 ( 169) hydrogen bonds : angle 5.13898 / 3.45 ( 471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6617 (mt) cc_final: 0.6326 (mt) REVERT: A 102 PHE cc_start: 0.8780 (m-80) cc_final: 0.8315 (m-80) REVERT: A 120 MET cc_start: 0.9419 (tpt) cc_final: 0.9049 (tpp) REVERT: A 155 GLU cc_start: 0.9051 (tt0) cc_final: 0.8806 (tt0) REVERT: A 183 THR cc_start: 0.8892 (t) cc_final: 0.8357 (t) REVERT: A 216 ASN cc_start: 0.8119 (t0) cc_final: 0.7570 (m-40) REVERT: A 221 TRP cc_start: 0.8803 (m100) cc_final: 0.8148 (m100) REVERT: A 222 TRP cc_start: 0.8873 (t-100) cc_final: 0.8501 (t-100) REVERT: A 231 MET cc_start: 0.9079 (mtm) cc_final: 0.8519 (mtt) REVERT: A 270 ARG cc_start: 0.8624 (mpt-90) cc_final: 0.8224 (mmt90) REVERT: A 301 ASP cc_start: 0.8412 (t0) cc_final: 0.8088 (p0) REVERT: B 111 TYR cc_start: 0.6583 (t80) cc_final: 0.6247 (t80) REVERT: B 133 ASN cc_start: 0.8985 (m110) cc_final: 0.8771 (t0) REVERT: B 172 PHE cc_start: 0.9292 (t80) cc_final: 0.8742 (t80) REVERT: B 234 MET cc_start: 0.4824 (ptt) cc_final: 0.3512 (ptt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0929 time to fit residues: 10.6358 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.140377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.083709 restraints weight = 26572.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.090528 restraints weight = 14598.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.095659 restraints weight = 10034.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.099376 restraints weight = 7753.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.102103 restraints weight = 6415.432| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4160 Z= 0.160 Angle : 0.678 7.434 5633 Z= 0.349 Chirality : 0.045 0.158 599 Planarity : 0.005 0.060 718 Dihedral : 8.064 79.806 590 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.12 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.16 (0.38), residues: 490 helix: 0.36 (0.36), residues: 192 sheet: 0.33 (0.68), residues: 58 loop : -0.52 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 239 TYR 0.016 0.002 TYR B 229 PHE 0.025 0.002 PHE A 238 TRP 0.015 0.002 TRP A 302 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 4160) covalent geometry : angle 0.67767 / 0.35 ( 5633) hydrogen bonds : bond 0.03832 / 2.51 ( 169) hydrogen bonds : angle 5.44504 / 3.70 ( 471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6563 (mt) cc_final: 0.6255 (mt) REVERT: A 102 PHE cc_start: 0.8798 (m-80) cc_final: 0.8379 (m-80) REVERT: A 120 MET cc_start: 0.9442 (tpt) cc_final: 0.9074 (tpp) REVERT: A 128 MET cc_start: 0.8688 (tmm) cc_final: 0.8191 (tmm) REVERT: A 155 GLU cc_start: 0.9094 (tt0) cc_final: 0.8844 (tt0) REVERT: A 183 THR cc_start: 0.9027 (t) cc_final: 0.8805 (t) REVERT: A 205 LEU cc_start: 0.7816 (mm) cc_final: 0.7531 (mm) REVERT: A 216 ASN cc_start: 0.8148 (t0) cc_final: 0.7350 (m-40) REVERT: A 221 TRP cc_start: 0.8819 (m100) cc_final: 0.8165 (m100) REVERT: A 222 TRP cc_start: 0.8833 (t-100) cc_final: 0.8375 (t-100) REVERT: A 231 MET cc_start: 0.9161 (mtm) cc_final: 0.8784 (mmm) REVERT: A 301 ASP cc_start: 0.8413 (t0) cc_final: 0.8097 (p0) REVERT: B 111 TYR cc_start: 0.6778 (t80) cc_final: 0.6227 (t80) REVERT: B 133 ASN cc_start: 0.8978 (m110) cc_final: 0.8760 (t0) REVERT: B 172 PHE cc_start: 0.9287 (t80) cc_final: 0.8788 (t80) REVERT: B 194 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8867 (tp30) REVERT: B 234 MET cc_start: 0.5006 (ptt) cc_final: 0.3740 (ptt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0744 time to fit residues: 8.8108 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.143266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.082543 restraints weight = 34548.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.090794 restraints weight = 16561.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.096721 restraints weight = 10685.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.100876 restraints weight = 7952.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.104245 restraints weight = 6444.909| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.4102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4160 Z= 0.127 Angle : 0.642 8.819 5633 Z= 0.325 Chirality : 0.044 0.137 599 Planarity : 0.005 0.057 718 Dihedral : 7.715 82.137 590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.71 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -0.08 (0.39), residues: 490 helix: 0.40 (0.37), residues: 192 sheet: 0.24 (0.68), residues: 58 loop : -0.40 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 239 TYR 0.013 0.001 TYR B 173 PHE 0.014 0.001 PHE A 129 TRP 0.014 0.001 TRP A 302 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4160) covalent geometry : angle 0.64175 / 0.33 ( 5633) hydrogen bonds : bond 0.03419 / 2.24 ( 169) hydrogen bonds : angle 5.26777 / 3.56 ( 471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6457 (mt) cc_final: 0.6101 (mt) REVERT: A 102 PHE cc_start: 0.8736 (m-80) cc_final: 0.8327 (m-80) REVERT: A 120 MET cc_start: 0.9447 (tpt) cc_final: 0.9120 (tpp) REVERT: A 128 MET cc_start: 0.8212 (tmm) cc_final: 0.7716 (tmm) REVERT: A 183 THR cc_start: 0.8863 (t) cc_final: 0.8542 (t) REVERT: A 205 LEU cc_start: 0.7991 (mm) cc_final: 0.7706 (mm) REVERT: A 211 LEU cc_start: 0.9341 (mm) cc_final: 0.8977 (mm) REVERT: A 216 ASN cc_start: 0.8046 (t0) cc_final: 0.7295 (m-40) REVERT: A 222 TRP cc_start: 0.8893 (t-100) cc_final: 0.8450 (t-100) REVERT: A 231 MET cc_start: 0.9145 (mtm) cc_final: 0.8774 (mmm) REVERT: A 301 ASP cc_start: 0.8358 (t0) cc_final: 0.8042 (p0) REVERT: B 111 TYR cc_start: 0.6909 (t80) cc_final: 0.6486 (t80) REVERT: B 172 PHE cc_start: 0.9224 (t80) cc_final: 0.8736 (t80) REVERT: B 194 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8993 (tp30) REVERT: B 234 MET cc_start: 0.5450 (ptt) cc_final: 0.4019 (ptt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0861 time to fit residues: 9.8897 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.131326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.075116 restraints weight = 34866.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.082235 restraints weight = 17960.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087229 restraints weight = 12167.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.090640 restraints weight = 9377.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.093454 restraints weight = 7789.526| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 4160 Z= 0.331 Angle : 0.942 17.171 5633 Z= 0.474 Chirality : 0.050 0.190 599 Planarity : 0.007 0.093 718 Dihedral : 9.371 76.905 590 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.11 (0.37), residues: 490 helix: -0.69 (0.34), residues: 207 sheet: -0.12 (0.70), residues: 48 loop : -0.78 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 239 TYR 0.019 0.003 TYR B 103 PHE 0.034 0.004 PHE A 238 TRP 0.031 0.004 TRP A 30 HIS 0.013 0.003 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.33 ( 4160) covalent geometry : angle 0.94183 / 0.47 ( 5633) hydrogen bonds : bond 0.05114 / 3.39 ( 169) hydrogen bonds : angle 6.39067 / 4.28 ( 471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8313 (tpt) cc_final: 0.8088 (tpp) REVERT: A 102 PHE cc_start: 0.8751 (m-80) cc_final: 0.8346 (m-80) REVERT: A 128 MET cc_start: 0.8546 (tmm) cc_final: 0.8205 (tmm) REVERT: A 155 GLU cc_start: 0.9270 (tt0) cc_final: 0.9040 (tt0) REVERT: A 216 ASN cc_start: 0.8212 (t0) cc_final: 0.7389 (m-40) REVERT: A 217 LYS cc_start: 0.8944 (mppt) cc_final: 0.8710 (mmtm) REVERT: A 221 TRP cc_start: 0.8857 (m100) cc_final: 0.8209 (m100) REVERT: A 222 TRP cc_start: 0.8565 (t-100) cc_final: 0.8071 (t-100) REVERT: A 231 MET cc_start: 0.9307 (mtm) cc_final: 0.9036 (mmm) REVERT: B 172 PHE cc_start: 0.9102 (t80) cc_final: 0.8832 (t80) REVERT: B 234 MET cc_start: 0.5959 (ptt) cc_final: 0.5530 (ptt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0738 time to fit residues: 8.2192 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.0060 chunk 38 optimal weight: 0.0020 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.145639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.079472 restraints weight = 35128.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.088227 restraints weight = 16795.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.094409 restraints weight = 10897.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.098614 restraints weight = 8202.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.101726 restraints weight = 6756.987| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.4035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.7565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4160 Z= 0.142 Angle : 0.745 10.414 5633 Z= 0.376 Chirality : 0.048 0.155 599 Planarity : 0.005 0.052 718 Dihedral : 8.420 83.327 590 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.95 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.38), residues: 490 helix: -0.17 (0.37), residues: 199 sheet: -0.34 (0.70), residues: 52 loop : -0.67 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 209 TYR 0.025 0.002 TYR B 229 PHE 0.034 0.002 PHE A 129 TRP 0.024 0.002 TRP A 30 HIS 0.011 0.002 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4160) covalent geometry : angle 0.74490 / 0.38 ( 5633) hydrogen bonds : bond 0.03878 / 2.53 ( 169) hydrogen bonds : angle 5.76608 / 3.86 ( 471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.8398 (m-80) cc_final: 0.8085 (m-80) REVERT: A 120 MET cc_start: 0.9446 (tpt) cc_final: 0.9124 (tpp) REVERT: A 128 MET cc_start: 0.8463 (tmm) cc_final: 0.7886 (tmm) REVERT: A 155 GLU cc_start: 0.9162 (tt0) cc_final: 0.8960 (tt0) REVERT: A 216 ASN cc_start: 0.8091 (t0) cc_final: 0.7341 (m-40) REVERT: A 222 TRP cc_start: 0.8581 (t-100) cc_final: 0.7645 (t-100) REVERT: A 231 MET cc_start: 0.9183 (mtm) cc_final: 0.8858 (mmm) REVERT: A 250 ILE cc_start: 0.7775 (mt) cc_final: 0.7462 (mt) REVERT: B 111 TYR cc_start: 0.7153 (t80) cc_final: 0.6754 (t80) REVERT: B 172 PHE cc_start: 0.9087 (t80) cc_final: 0.8725 (t80) REVERT: B 234 MET cc_start: 0.5709 (ptt) cc_final: 0.5252 (ptt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0715 time to fit residues: 8.7771 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.138631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.077970 restraints weight = 34353.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.086142 restraints weight = 16757.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.091592 restraints weight = 11117.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.095372 restraints weight = 8530.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.097964 restraints weight = 7105.662| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4160 Z= 0.182 Angle : 0.744 10.425 5633 Z= 0.378 Chirality : 0.046 0.157 599 Planarity : 0.005 0.054 718 Dihedral : 8.551 79.878 590 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.74 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.90 (0.38), residues: 490 helix: -0.37 (0.36), residues: 201 sheet: -0.45 (0.70), residues: 52 loop : -0.71 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 93 TYR 0.029 0.002 TYR B 229 PHE 0.028 0.002 PHE A 129 TRP 0.027 0.003 TRP A 30 HIS 0.006 0.002 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 4160) covalent geometry : angle 0.74402 / 0.38 ( 5633) hydrogen bonds : bond 0.03976 / 2.61 ( 169) hydrogen bonds : angle 5.93921 / 3.96 ( 471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.88 seconds wall clock time: 20 minutes 4.75 seconds (1204.75 seconds total)