Starting phenix.real_space_refine on Fri May 9 22:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_47944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_47944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_47944.map" model { file = "/net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_47944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edc_47944/05_2025/9edc_47944.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.07, per 1000 atoms: 1.00 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: 0.99 Conformation dependent library (CDL) restraints added in 701.4 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: 0.41 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: 0.99 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.120 Find NCS groups from input model: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (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 TRP 0.021 0.002 TRP A 30 HIS 0.005 0.001 HIS A 142 PHE 0.020 0.002 PHE A 145 TYR 0.019 0.002 TYR B 229 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.16350 ( 169) hydrogen bonds : angle 6.50241 ( 471) covalent geometry : bond 0.00497 ( 4160) covalent geometry : angle 0.88266 ( 5633) *********************** 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 : 0.424 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: 0.6545 (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: 0.2619 time to fit residues: 46.3347 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 : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.149180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.095568 restraints weight = 17815.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.102021 restraints weight = 11307.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.106911 restraints weight = 8137.030| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4160 Z= 0.141 Angle : 0.667 7.893 5633 Z= 0.348 Chirality : 0.045 0.180 599 Planarity : 0.005 0.056 718 Dihedral : 8.270 85.842 590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.36), residues: 490 helix: -0.26 (0.35), residues: 201 sheet: 1.25 (0.74), residues: 43 loop : -0.65 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 30 HIS 0.007 0.001 HIS A 142 PHE 0.043 0.002 PHE A 129 TYR 0.024 0.002 TYR A 247 ARG 0.006 0.001 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 169) hydrogen bonds : angle 5.24541 ( 471) covalent geometry : bond 0.00310 ( 4160) covalent geometry : angle 0.66719 ( 5633) *********************** 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 117 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.416 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6863 (mt) cc_final: 0.6567 (mt) REVERT: A 58 MET cc_start: 0.8767 (mmp) cc_final: 0.8521 (tpt) REVERT: A 167 LEU cc_start: 0.8790 (tp) cc_final: 0.8344 (tp) REVERT: A 168 LYS cc_start: 0.9105 (pttt) cc_final: 0.8816 (pttt) REVERT: A 216 ASN cc_start: 0.8932 (p0) cc_final: 0.8622 (p0) REVERT: A 221 TRP cc_start: 0.8963 (m100) cc_final: 0.8232 (m100) REVERT: A 222 TRP cc_start: 0.9090 (t-100) cc_final: 0.8820 (t-100) REVERT: A 231 MET cc_start: 0.9085 (mtm) cc_final: 0.8858 (mtm) REVERT: A 324 THR cc_start: 0.8217 (t) cc_final: 0.7963 (m) REVERT: B 94 ARG cc_start: 0.7857 (tmt-80) cc_final: 0.7455 (tmt170) REVERT: B 172 PHE cc_start: 0.9302 (t80) cc_final: 0.8611 (t80) REVERT: B 224 ILE cc_start: 0.8983 (tp) cc_final: 0.8450 (tp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2519 time to fit residues: 33.8652 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.147882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.089238 restraints weight = 29767.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.097192 restraints weight = 15186.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.103250 restraints weight = 9945.614| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 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 = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4160 Z= 0.136 Angle : 0.634 7.721 5633 Z= 0.335 Chirality : 0.045 0.179 599 Planarity : 0.005 0.061 718 Dihedral : 8.068 82.955 590 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.37), residues: 490 helix: 0.22 (0.36), residues: 200 sheet: 1.13 (0.73), residues: 43 loop : -0.46 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 302 HIS 0.005 0.001 HIS A 142 PHE 0.025 0.002 PHE A 129 TYR 0.021 0.002 TYR A 247 ARG 0.006 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 169) hydrogen bonds : angle 5.01927 ( 471) covalent geometry : bond 0.00305 ( 4160) covalent geometry : angle 0.63405 ( 5633) *********************** 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 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.419 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: A 19 LEU cc_start: 0.7000 (mt) cc_final: 0.6759 (mt) REVERT: A 102 PHE cc_start: 0.8307 (m-80) cc_final: 0.7959 (m-80) REVERT: A 216 ASN cc_start: 0.8510 (p0) cc_final: 0.7930 (m-40) REVERT: A 221 TRP cc_start: 0.8314 (m100) cc_final: 0.7781 (m100) REVERT: A 231 MET cc_start: 0.8917 (mtm) cc_final: 0.8637 (mtm) REVERT: A 324 THR cc_start: 0.8208 (t) cc_final: 0.7980 (m) REVERT: B 94 ARG cc_start: 0.7727 (tmt-80) cc_final: 0.7443 (tmt170) REVERT: B 172 PHE cc_start: 0.9115 (t80) cc_final: 0.8543 (t80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2591 time to fit residues: 29.0985 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 0.0020 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS B 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.141736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082911 restraints weight = 40582.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.091288 restraints weight = 18290.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.097286 restraints weight = 11439.467| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 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 = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4160 Z= 0.159 Angle : 0.648 7.570 5633 Z= 0.339 Chirality : 0.045 0.157 599 Planarity : 0.005 0.059 718 Dihedral : 7.870 80.011 590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.06 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.37), residues: 490 helix: 0.19 (0.36), residues: 200 sheet: 0.81 (0.79), residues: 38 loop : -0.48 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 302 HIS 0.004 0.001 HIS A 158 PHE 0.027 0.002 PHE A 129 TYR 0.018 0.002 TYR A 247 ARG 0.012 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 169) hydrogen bonds : angle 5.17681 ( 471) covalent geometry : bond 0.00344 ( 4160) covalent geometry : angle 0.64836 ( 5633) *********************** 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 97 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.421 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: A 102 PHE cc_start: 0.8502 (m-80) cc_final: 0.7311 (m-80) REVERT: A 152 LEU cc_start: 0.9646 (mt) cc_final: 0.9431 (mt) REVERT: A 183 THR cc_start: 0.8572 (t) cc_final: 0.8154 (t) REVERT: A 217 LYS cc_start: 0.8350 (mppt) cc_final: 0.8063 (mmtm) REVERT: A 221 TRP cc_start: 0.8949 (m100) cc_final: 0.8275 (m100) REVERT: A 222 TRP cc_start: 0.8775 (t-100) cc_final: 0.8454 (t-100) REVERT: A 231 MET cc_start: 0.9155 (mtm) cc_final: 0.8826 (mtm) REVERT: A 308 ARG cc_start: 0.9026 (ptm160) cc_final: 0.8756 (mtt90) REVERT: A 324 THR cc_start: 0.8159 (t) cc_final: 0.7888 (m) REVERT: B 172 PHE cc_start: 0.9401 (t80) cc_final: 0.8948 (t80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2376 time to fit residues: 26.9745 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.138507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.085863 restraints weight = 27846.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092873 restraints weight = 14743.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.097810 restraints weight = 10025.254| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4160 Z= 0.216 Angle : 0.713 7.731 5633 Z= 0.376 Chirality : 0.047 0.187 599 Planarity : 0.006 0.069 718 Dihedral : 8.077 77.827 590 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.89 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.36), residues: 490 helix: -0.09 (0.35), residues: 191 sheet: 0.09 (0.69), residues: 48 loop : -0.62 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 30 HIS 0.003 0.001 HIS A 294 PHE 0.018 0.003 PHE A 138 TYR 0.037 0.003 TYR A 247 ARG 0.010 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 169) hydrogen bonds : angle 5.49086 ( 471) covalent geometry : bond 0.00455 ( 4160) covalent geometry : angle 0.71345 ( 5633) *********************** 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 : 0.452 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 102 PHE cc_start: 0.8552 (m-80) cc_final: 0.8225 (m-80) REVERT: A 152 LEU cc_start: 0.9636 (mt) cc_final: 0.9391 (mt) REVERT: A 205 LEU cc_start: 0.7817 (mm) cc_final: 0.7399 (mm) REVERT: A 221 TRP cc_start: 0.8874 (m100) cc_final: 0.8187 (m100) REVERT: A 222 TRP cc_start: 0.8916 (t-100) cc_final: 0.8325 (t-100) REVERT: A 231 MET cc_start: 0.9223 (mtm) cc_final: 0.8941 (mmm) REVERT: B 172 PHE cc_start: 0.9333 (t80) cc_final: 0.8900 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2425 time to fit residues: 28.7027 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4586 r_free = 0.4586 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.083261 restraints weight = 33485.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.091255 restraints weight = 16572.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.096798 restraints weight = 10873.829| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4160 Z= 0.152 Angle : 0.664 7.970 5633 Z= 0.344 Chirality : 0.045 0.166 599 Planarity : 0.005 0.066 718 Dihedral : 7.421 80.830 590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.68 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.37), residues: 490 helix: -0.06 (0.34), residues: 192 sheet: 0.13 (0.72), residues: 48 loop : -0.57 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 30 HIS 0.007 0.001 HIS A 158 PHE 0.027 0.002 PHE A 129 TYR 0.028 0.002 TYR A 247 ARG 0.006 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 169) hydrogen bonds : angle 5.43287 ( 471) covalent geometry : bond 0.00335 ( 4160) covalent geometry : angle 0.66423 ( 5633) *********************** 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 99 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.474 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 102 PHE cc_start: 0.8563 (m-80) cc_final: 0.8236 (m-80) REVERT: A 152 LEU cc_start: 0.9668 (mt) cc_final: 0.9445 (mt) REVERT: A 205 LEU cc_start: 0.7587 (mm) cc_final: 0.7375 (mm) REVERT: A 221 TRP cc_start: 0.8903 (m100) cc_final: 0.8273 (m100) REVERT: A 222 TRP cc_start: 0.8890 (t-100) cc_final: 0.8210 (t-100) REVERT: A 231 MET cc_start: 0.9322 (mtm) cc_final: 0.8684 (mtm) REVERT: A 324 THR cc_start: 0.8120 (t) cc_final: 0.7866 (m) REVERT: B 172 PHE cc_start: 0.9288 (t80) cc_final: 0.8868 (t80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2314 time to fit residues: 26.8363 Evaluate side-chains 72 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.144323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.085834 restraints weight = 36040.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.094024 restraints weight = 16939.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.100049 restraints weight = 10814.009| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 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 = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.6622 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= 0.130 Angle : 0.636 7.411 5633 Z= 0.330 Chirality : 0.045 0.152 599 Planarity : 0.005 0.068 718 Dihedral : 7.271 82.823 590 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.38), residues: 490 helix: 0.14 (0.36), residues: 194 sheet: 0.48 (0.69), residues: 53 loop : -0.57 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 30 HIS 0.006 0.001 HIS A 158 PHE 0.018 0.002 PHE A 238 TYR 0.021 0.002 TYR A 247 ARG 0.005 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 169) hydrogen bonds : angle 5.35207 ( 471) covalent geometry : bond 0.00291 ( 4160) covalent geometry : angle 0.63636 ( 5633) *********************** 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 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.462 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 102 PHE cc_start: 0.8625 (m-80) cc_final: 0.8373 (m-80) REVERT: A 137 ARG cc_start: 0.6854 (mmp80) cc_final: 0.6491 (mmp80) REVERT: A 152 LEU cc_start: 0.9676 (mt) cc_final: 0.9452 (mt) REVERT: A 221 TRP cc_start: 0.8869 (m100) cc_final: 0.8192 (m100) REVERT: A 222 TRP cc_start: 0.8809 (t-100) cc_final: 0.8080 (t-100) REVERT: A 231 MET cc_start: 0.9329 (mtm) cc_final: 0.8672 (mtm) REVERT: A 324 THR cc_start: 0.8133 (t) cc_final: 0.7872 (m) REVERT: B 172 PHE cc_start: 0.9265 (t80) cc_final: 0.8856 (t80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2081 time to fit residues: 23.4129 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 44 optimal weight: 0.1980 chunk 46 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.147203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.092024 restraints weight = 18003.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.098474 restraints weight = 11336.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.103107 restraints weight = 8208.642| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4088 r_free = 0.4088 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 = 0.4088 r_free = 0.4088 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.6852 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= 0.123 Angle : 0.652 10.259 5633 Z= 0.329 Chirality : 0.046 0.140 599 Planarity : 0.005 0.064 718 Dihedral : 7.093 85.234 590 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.38), residues: 490 helix: 0.25 (0.37), residues: 194 sheet: 0.58 (0.71), residues: 53 loop : -0.59 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 30 HIS 0.006 0.002 HIS A 158 PHE 0.018 0.001 PHE A 238 TYR 0.017 0.002 TYR A 247 ARG 0.005 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 169) hydrogen bonds : angle 5.26107 ( 471) covalent geometry : bond 0.00284 ( 4160) covalent geometry : angle 0.65233 ( 5633) *********************** 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 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.432 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 102 PHE cc_start: 0.8058 (m-80) cc_final: 0.7559 (m-80) REVERT: A 137 ARG cc_start: 0.7052 (mmp80) cc_final: 0.6520 (mmp80) REVERT: A 152 LEU cc_start: 0.9555 (mt) cc_final: 0.9299 (mt) REVERT: A 183 THR cc_start: 0.8490 (t) cc_final: 0.8213 (t) REVERT: A 222 TRP cc_start: 0.8180 (t-100) cc_final: 0.7782 (t-100) REVERT: A 231 MET cc_start: 0.9063 (mtm) cc_final: 0.8387 (mtm) REVERT: A 308 ARG cc_start: 0.9057 (ptm160) cc_final: 0.8633 (mtt180) REVERT: A 324 THR cc_start: 0.8203 (t) cc_final: 0.7952 (m) REVERT: B 111 TYR cc_start: 0.6487 (t80) cc_final: 0.6276 (t80) REVERT: B 164 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9124 (tp40) REVERT: B 172 PHE cc_start: 0.9085 (t80) cc_final: 0.8657 (t80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2131 time to fit residues: 24.0164 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4611 r_free = 0.4611 target = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.083747 restraints weight = 36127.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.092655 restraints weight = 16534.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.098733 restraints weight = 10362.976| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 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 = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.3977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4160 Z= 0.152 Angle : 0.677 9.633 5633 Z= 0.345 Chirality : 0.045 0.154 599 Planarity : 0.005 0.058 718 Dihedral : 7.275 80.440 590 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.92 % Favored : 95.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.38), residues: 490 helix: 0.29 (0.37), residues: 194 sheet: 0.58 (0.72), residues: 51 loop : -0.64 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 30 HIS 0.004 0.001 HIS A 131 PHE 0.036 0.002 PHE A 129 TYR 0.021 0.002 TYR A 247 ARG 0.004 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 169) hydrogen bonds : angle 5.54304 ( 471) covalent geometry : bond 0.00335 ( 4160) covalent geometry : angle 0.67697 ( 5633) *********************** 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 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.522 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 102 PHE cc_start: 0.8659 (m-80) cc_final: 0.8441 (m-80) REVERT: A 137 ARG cc_start: 0.7533 (mmp80) cc_final: 0.6933 (mmp80) REVERT: A 152 LEU cc_start: 0.9682 (mt) cc_final: 0.9421 (mt) REVERT: A 222 TRP cc_start: 0.8697 (t-100) cc_final: 0.7929 (t-100) REVERT: A 231 MET cc_start: 0.8964 (mtm) cc_final: 0.8652 (ttt) REVERT: B 111 TYR cc_start: 0.7054 (t80) cc_final: 0.6829 (t80) REVERT: B 172 PHE cc_start: 0.9232 (t80) cc_final: 0.8841 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2417 time to fit residues: 25.5186 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.141776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084779 restraints weight = 30099.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093026 restraints weight = 15005.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.098668 restraints weight = 9812.023| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4160 Z= 0.166 Angle : 0.709 10.827 5633 Z= 0.359 Chirality : 0.046 0.230 599 Planarity : 0.005 0.056 718 Dihedral : 7.940 80.001 590 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.74 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.37), residues: 490 helix: 0.15 (0.36), residues: 193 sheet: 0.43 (0.72), residues: 51 loop : -0.69 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 30 HIS 0.004 0.001 HIS B 138 PHE 0.023 0.002 PHE A 129 TYR 0.021 0.002 TYR A 247 ARG 0.012 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 169) hydrogen bonds : angle 5.68605 ( 471) covalent geometry : bond 0.00368 ( 4160) covalent geometry : angle 0.70869 ( 5633) ********************** 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 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.437 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 102 PHE cc_start: 0.8596 (m-80) cc_final: 0.8363 (m-80) REVERT: A 137 ARG cc_start: 0.7527 (mmp80) cc_final: 0.7108 (mmp80) REVERT: A 152 LEU cc_start: 0.9682 (mt) cc_final: 0.9432 (mt) REVERT: A 222 TRP cc_start: 0.8792 (t-100) cc_final: 0.7941 (t-100) REVERT: A 231 MET cc_start: 0.8941 (mtm) cc_final: 0.8625 (ttt) REVERT: B 172 PHE cc_start: 0.9192 (t80) cc_final: 0.8851 (t80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2370 time to fit residues: 26.3089 Evaluate side-chains 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 46 optimal weight: 9.9990 overall best weight: 1.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 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 = 0.4609 r_free = 0.4609 target = 0.141424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.083066 restraints weight = 31639.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.091580 restraints weight = 15231.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.097365 restraints weight = 9814.046| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 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 = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.3975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4160 Z= 0.144 Angle : 0.682 10.735 5633 Z= 0.345 Chirality : 0.045 0.163 599 Planarity : 0.005 0.057 718 Dihedral : 7.515 80.865 590 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.92 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.38), residues: 490 helix: 0.13 (0.36), residues: 193 sheet: 0.56 (0.73), residues: 51 loop : -0.69 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 30 HIS 0.005 0.001 HIS A 131 PHE 0.024 0.002 PHE A 129 TYR 0.016 0.002 TYR B 173 ARG 0.005 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 169) hydrogen bonds : angle 5.70440 ( 471) covalent geometry : bond 0.00325 ( 4160) covalent geometry : angle 0.68201 ( 5633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.36 seconds wall clock time: 43 minutes 18.58 seconds (2598.58 seconds total)