Starting phenix.real_space_refine on Thu Jul 2 00:50:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5r_63881/07_2026/9u5r_63881.cif" } resolution = 3.59 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= 0.001 sd= 1.007 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 75 5.49 5 S 15 5.16 5 C 2692 2.51 5 N 816 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4743 Number of models: 1 Model: "" Number of chains: 4 Chain: "O" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 792 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.32 Number of scatterers: 4743 At special positions: 0 Unit cell: (82.56, 88.32, 109.44, 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 15 16.00 P 75 15.00 O 1145 8.00 N 816 7.00 C 2692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P 24 " - pdb=" SG CYS P 98 " distance=2.99 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: 0.32 Conformation dependent library (CDL) restraints added in 112.5 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.9% alpha, 44.2% beta 26 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 38 through 42 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.882A pdb=" N ILE O 90 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 93 removed outlier: 3.791A pdb=" N THR P 93 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.837A pdb=" N ASP Q 29 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 removed outlier: 4.019A pdb=" N GLU Q 82 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 15 through 20 removed outlier: 6.956A pdb=" N VAL O 34 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 70 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU O 62 " --> pdb=" O LEU O 70 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU O 72 " --> pdb=" O TYR O 60 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR O 60 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL O 74 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP O 58 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR O 76 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL O 56 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 119 through 120 removed outlier: 3.748A pdb=" N THR O 119 " --> pdb=" O ARG O 136 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA O 171 " --> pdb=" O HIS O 160 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N HIS O 160 " --> pdb=" O ALA O 171 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE O 156 " --> pdb=" O ALA O 152 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA O 152 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY O 158 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER O 105 " --> pdb=" O THR O 109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR O 109 " --> pdb=" O SER O 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 123 through 126 removed outlier: 3.752A pdb=" N ILE O 124 " --> pdb=" O THR O 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 131 " --> pdb=" O ILE O 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 5 through 10 Processing sheet with id=AA5, first strand: chain 'P' and resid 12 through 14 removed outlier: 3.660A pdb=" N GLY P 12 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR P 125 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET P 36 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL P 52 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP P 38 " --> pdb=" O VAL P 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR Q 31 " --> pdb=" O TRP Q 90 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TRP Q 34 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1217 1.34 - 1.46: 1487 1.46 - 1.58: 2113 1.58 - 1.70: 148 1.70 - 1.82: 22 Bond restraints: 4987 Sorted by residual: bond pdb=" C VAL Q 3 " pdb=" O VAL Q 3 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" CA PRO Q 7 " pdb=" C PRO Q 7 " ideal model delta sigma weight residual 1.514 1.495 0.019 5.50e-03 3.31e+04 1.25e+01 bond pdb=" C TYR Q 2 " pdb=" O TYR Q 2 " ideal model delta sigma weight residual 1.234 1.278 -0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA SER Q 11 " pdb=" CB SER Q 11 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.76e-02 3.23e+03 8.62e+00 bond pdb=" N GLN P 8 " pdb=" CA GLN P 8 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.26e+00 ... (remaining 4982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6814 2.08 - 4.15: 261 4.15 - 6.23: 27 6.23 - 8.31: 2 8.31 - 10.39: 2 Bond angle restraints: 7106 Sorted by residual: angle pdb=" N1 C R 74 " pdb=" C2 C R 74 " pdb=" O2 C R 74 " ideal model delta sigma weight residual 118.90 121.23 -2.33 6.00e-01 2.78e+00 1.51e+01 angle pdb=" C1' C R 74 " pdb=" N1 C R 74 " pdb=" C2 C R 74 " ideal model delta sigma weight residual 118.80 123.03 -4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" N TYR P 97 " pdb=" CA TYR P 97 " pdb=" C TYR P 97 " ideal model delta sigma weight residual 110.42 116.36 -5.94 1.55e+00 4.16e-01 1.47e+01 angle pdb=" N TYR P 96 " pdb=" CA TYR P 96 " pdb=" C TYR P 96 " ideal model delta sigma weight residual 108.90 114.59 -5.69 1.63e+00 3.76e-01 1.22e+01 angle pdb=" CB MET Q 80 " pdb=" CG MET Q 80 " pdb=" SD MET Q 80 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 7101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 2718 26.25 - 52.49: 217 52.49 - 78.74: 133 78.74 - 104.99: 5 104.99 - 131.24: 1 Dihedral angle restraints: 3074 sinusoidal: 1910 harmonic: 1164 Sorted by residual: dihedral pdb=" O4' A R 36 " pdb=" C1' A R 36 " pdb=" N9 A R 36 " pdb=" C4 A R 36 " ideal model delta sinusoidal sigma weight residual -106.00 -178.10 72.10 1 1.70e+01 3.46e-03 2.30e+01 dihedral pdb=" CB CYS P 24 " pdb=" SG CYS P 24 " pdb=" SG CYS P 98 " pdb=" CB CYS P 98 " ideal model delta sinusoidal sigma weight residual 93.00 56.89 36.11 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" C4' U R 14 " pdb=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sinusoidal sigma weight residual 220.00 88.76 131.24 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 3071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 704 0.107 - 0.214: 140 0.214 - 0.321: 12 0.321 - 0.428: 2 0.428 - 0.534: 2 Chirality restraints: 860 Sorted by residual: chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" P A R 32 " pdb=" OP1 A R 32 " pdb=" OP2 A R 32 " pdb=" O5' A R 32 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 857 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 37 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO O 38 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 79 " 0.161 9.50e-02 1.11e+02 7.20e-02 3.19e+00 pdb=" NE ARG O 79 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG O 79 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG O 79 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG O 79 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 7 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C LEU P 7 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU P 7 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN P 8 " 0.009 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 39 2.54 - 3.13: 3445 3.13 - 3.72: 7896 3.72 - 4.31: 10450 4.31 - 4.90: 16042 Nonbonded interactions: 37872 Sorted by model distance: nonbonded pdb=" OD1 ASP O 64 " pdb=" CD PRO O 65 " model vdw 1.945 3.440 nonbonded pdb=" O ASP O 93 " pdb=" OD1 ASP O 93 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR O 26 " pdb=" OG SER O 105 " model vdw 2.240 3.040 nonbonded pdb=" OG SER P 19 " pdb=" OE1 GLN P 84 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP P 75 " pdb=" NZ LYS P 78 " model vdw 2.257 3.120 ... (remaining 37867 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.680 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5151 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 : 0.015 0.958 4988 Z= 0.796 Angle : 0.912 10.960 7108 Z= 0.567 Chirality : 0.081 0.534 860 Planarity : 0.005 0.072 635 Dihedral : 21.108 131.235 2337 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 25.22 % Favored : 74.78 % 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: -0.34 (0.44), residues: 408 helix: 0.40 (1.53), residues: 12 sheet: 0.04 (0.42), residues: 171 loop : -0.40 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG O 84 TYR 0.021 0.002 TYR O 60 PHE 0.008 0.001 PHE O 178 TRP 0.009 0.002 TRP Q 90 HIS 0.005 0.001 HIS O 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.42 ( 4987) covalent geometry : angle 0.90247 / 0.56 ( 7106) SS BOND : bond 0.95774 / 63.85 ( 1) SS BOND : angle 7.80458 / 4.13 ( 2) hydrogen bonds : bond 0.14833 / 9.13 ( 186) hydrogen bonds : angle 5.96863 / 4.61 ( 423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: O 13 LYS cc_start: 0.7342 (mttt) cc_final: 0.6726 (mttt) REVERT: O 14 ASN cc_start: 0.7351 (m110) cc_final: 0.6707 (t0) REVERT: O 134 MET cc_start: 0.7172 (mtm) cc_final: 0.6959 (ptt) REVERT: P 112 SER cc_start: 0.7727 (m) cc_final: 0.7351 (m) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0861 time to fit residues: 4.4752 Evaluate side-chains 39 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 37 optimal weight: 0.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 42 GLN O 80 ASN O 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.214231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.191821 restraints weight = 8515.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.195698 restraints weight = 4605.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.198319 restraints weight = 2866.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.200090 restraints weight = 1975.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.201249 restraints weight = 1480.749| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4988 Z= 0.194 Angle : 0.633 6.804 7108 Z= 0.354 Chirality : 0.041 0.249 860 Planarity : 0.006 0.050 635 Dihedral : 20.957 130.214 1625 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.64 % Allowed : 20.29 % Favored : 75.07 % 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 (0.42), residues: 408 helix: 1.65 (1.52), residues: 12 sheet: 0.26 (0.42), residues: 160 loop : -0.62 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 74 TYR 0.019 0.003 TYR O 139 PHE 0.015 0.002 PHE O 83 TRP 0.012 0.002 TRP P 38 HIS 0.004 0.002 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 4987) covalent geometry : angle 0.63082 / 0.35 ( 7106) SS BOND : bond 0.01786 / 1.19 ( 1) SS BOND : angle 3.45734 / 2.39 ( 2) hydrogen bonds : bond 0.05431 / 3.59 ( 186) hydrogen bonds : angle 4.88163 / 3.64 ( 423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.079 Fit side-chains REVERT: O 22 LYS cc_start: 0.7481 (mmmm) cc_final: 0.7068 (mtmt) outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.0554 time to fit residues: 3.9707 Evaluate side-chains 49 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 145 GLN P 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.208742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.185585 restraints weight = 9012.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.189441 restraints weight = 5033.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.191995 restraints weight = 3207.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.193763 restraints weight = 2267.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.194977 restraints weight = 1735.234| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4988 Z= 0.211 Angle : 0.663 8.631 7108 Z= 0.365 Chirality : 0.042 0.228 860 Planarity : 0.006 0.059 635 Dihedral : 20.762 131.606 1625 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.64 % Allowed : 20.29 % Favored : 75.07 % 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: -0.50 (0.41), residues: 408 helix: 2.23 (1.58), residues: 12 sheet: 0.40 (0.43), residues: 149 loop : -0.95 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 12 TYR 0.027 0.003 TYR P 96 PHE 0.018 0.002 PHE O 83 TRP 0.015 0.003 TRP Q 90 HIS 0.004 0.002 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 ( 4987) covalent geometry : angle 0.65983 / 0.36 ( 7106) SS BOND : bond 0.01955 / 1.30 ( 1) SS BOND : angle 3.65137 / 2.22 ( 2) hydrogen bonds : bond 0.06341 / 4.25 ( 186) hydrogen bonds : angle 4.89120 / 3.62 ( 423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.132 Fit side-chains REVERT: O 13 LYS cc_start: 0.7420 (mttt) cc_final: 0.7105 (mttt) REVERT: P 61 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: P 72 ILE cc_start: 0.4060 (OUTLIER) cc_final: 0.3560 (pt) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 0.0771 time to fit residues: 5.4222 Evaluate side-chains 55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 61 TYR Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 30 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4629 r_free = 0.4629 target = 0.210888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187818 restraints weight = 8579.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191838 restraints weight = 4708.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.194484 restraints weight = 2909.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.196262 restraints weight = 1990.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.197399 restraints weight = 1485.478| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4988 Z= 0.140 Angle : 0.553 6.232 7108 Z= 0.309 Chirality : 0.038 0.234 860 Planarity : 0.005 0.054 635 Dihedral : 20.752 131.646 1625 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.35 % Allowed : 21.45 % Favored : 74.20 % 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: -0.46 (0.41), residues: 408 helix: 2.67 (1.58), residues: 12 sheet: 0.42 (0.43), residues: 149 loop : -0.94 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 74 TYR 0.012 0.002 TYR Q 31 PHE 0.008 0.001 PHE O 25 TRP 0.012 0.002 TRP Q 90 HIS 0.003 0.001 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 4987) covalent geometry : angle 0.55280 / 0.31 ( 7106) SS BOND : bond 0.01117 / 0.74 ( 1) SS BOND : angle 1.65985 / 1.05 ( 2) hydrogen bonds : bond 0.05208 / 3.58 ( 186) hydrogen bonds : angle 4.72527 / 3.45 ( 423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.129 Fit side-chains REVERT: O 22 LYS cc_start: 0.7483 (mmmm) cc_final: 0.7015 (mtmt) REVERT: P 72 ILE cc_start: 0.3832 (OUTLIER) cc_final: 0.3241 (pt) outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.0822 time to fit residues: 5.3710 Evaluate side-chains 55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 120 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4629 r_free = 0.4629 target = 0.210330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.187685 restraints weight = 9070.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.191460 restraints weight = 5048.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194021 restraints weight = 3211.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.195806 restraints weight = 2253.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.196930 restraints weight = 1703.159| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4988 Z= 0.125 Angle : 0.533 6.589 7108 Z= 0.296 Chirality : 0.038 0.235 860 Planarity : 0.005 0.054 635 Dihedral : 20.691 132.357 1625 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.77 % Allowed : 25.22 % Favored : 71.01 % 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: -0.26 (0.42), residues: 408 helix: 3.02 (1.57), residues: 12 sheet: 0.54 (0.41), residues: 160 loop : -0.87 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 21 TYR 0.012 0.002 TYR P 82 PHE 0.018 0.002 PHE O 157 TRP 0.011 0.002 TRP Q 90 HIS 0.003 0.001 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 4987) covalent geometry : angle 0.53242 / 0.30 ( 7106) SS BOND : bond 0.00922 / 0.61 ( 1) SS BOND : angle 1.44795 / 0.88 ( 2) hydrogen bonds : bond 0.04957 / 3.46 ( 186) hydrogen bonds : angle 4.55500 / 3.34 ( 423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.160 Fit side-chains REVERT: O 22 LYS cc_start: 0.7475 (mmmm) cc_final: 0.7088 (mtmt) REVERT: P 72 ILE cc_start: 0.3603 (OUTLIER) cc_final: 0.3162 (pt) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.0714 time to fit residues: 4.5464 Evaluate side-chains 52 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 120 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4603 r_free = 0.4603 target = 0.208273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.186150 restraints weight = 8589.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.189881 restraints weight = 4624.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.192451 restraints weight = 2868.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.194140 restraints weight = 1968.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.195273 restraints weight = 1475.735| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4988 Z= 0.158 Angle : 0.569 7.747 7108 Z= 0.316 Chirality : 0.039 0.236 860 Planarity : 0.005 0.055 635 Dihedral : 20.667 133.258 1625 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.35 % Allowed : 24.35 % Favored : 71.30 % 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: -0.22 (0.42), residues: 408 helix: 3.18 (1.58), residues: 12 sheet: 0.60 (0.41), residues: 163 loop : -0.90 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 21 TYR 0.015 0.002 TYR Q 31 PHE 0.020 0.002 PHE O 157 TRP 0.014 0.002 TRP Q 90 HIS 0.004 0.001 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 4987) covalent geometry : angle 0.56849 / 0.32 ( 7106) SS BOND : bond 0.01125 / 0.75 ( 1) SS BOND : angle 1.81857 / 1.16 ( 2) hydrogen bonds : bond 0.05415 / 3.73 ( 186) hydrogen bonds : angle 4.61430 / 3.33 ( 423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.126 Fit side-chains REVERT: O 22 LYS cc_start: 0.7268 (mmmm) cc_final: 0.6903 (mtmt) REVERT: O 120 MET cc_start: 0.5183 (ppp) cc_final: 0.4698 (ppp) REVERT: P 61 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.6017 (m-10) REVERT: P 72 ILE cc_start: 0.3819 (OUTLIER) cc_final: 0.3351 (pt) outliers start: 15 outliers final: 13 residues processed: 57 average time/residue: 0.0754 time to fit residues: 5.5517 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 61 TYR Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4597 r_free = 0.4597 target = 0.207795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.186290 restraints weight = 8602.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.189988 restraints weight = 4725.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.192463 restraints weight = 2942.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.194124 restraints weight = 2022.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.195241 restraints weight = 1511.412| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4988 Z= 0.144 Angle : 0.560 8.149 7108 Z= 0.312 Chirality : 0.039 0.237 860 Planarity : 0.005 0.054 635 Dihedral : 20.637 133.247 1625 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.93 % Allowed : 25.22 % Favored : 69.86 % 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: -0.27 (0.42), residues: 408 helix: 3.26 (1.61), residues: 12 sheet: 0.44 (0.41), residues: 165 loop : -0.84 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 18 TYR 0.014 0.002 TYR P 96 PHE 0.020 0.002 PHE O 157 TRP 0.013 0.002 TRP Q 90 HIS 0.004 0.001 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4987) covalent geometry : angle 0.55997 / 0.31 ( 7106) SS BOND : bond 0.00946 / 0.63 ( 1) SS BOND : angle 1.46791 / 0.90 ( 2) hydrogen bonds : bond 0.05196 / 3.63 ( 186) hydrogen bonds : angle 4.59936 / 3.33 ( 423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.129 Fit side-chains REVERT: O 22 LYS cc_start: 0.7212 (mmmm) cc_final: 0.6710 (mtpt) REVERT: O 120 MET cc_start: 0.5053 (ppp) cc_final: 0.4576 (ppp) REVERT: P 72 ILE cc_start: 0.3739 (OUTLIER) cc_final: 0.3333 (pt) outliers start: 17 outliers final: 16 residues processed: 51 average time/residue: 0.0763 time to fit residues: 4.9873 Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 120 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 6 GLN ** Q 88 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 = 0.4579 r_free = 0.4579 target = 0.205955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.184184 restraints weight = 8589.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187815 restraints weight = 4708.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190237 restraints weight = 2942.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.191881 restraints weight = 2037.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.192983 restraints weight = 1535.721| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4988 Z= 0.167 Angle : 0.589 8.547 7108 Z= 0.329 Chirality : 0.040 0.237 860 Planarity : 0.005 0.054 635 Dihedral : 20.676 133.706 1625 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.93 % Allowed : 25.51 % Favored : 69.57 % 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: -0.46 (0.42), residues: 408 helix: 3.23 (1.61), residues: 12 sheet: 0.19 (0.41), residues: 169 loop : -0.87 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 74 TYR 0.015 0.002 TYR O 139 PHE 0.023 0.002 PHE O 157 TRP 0.015 0.002 TRP Q 90 HIS 0.004 0.002 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 4987) covalent geometry : angle 0.58794 / 0.33 ( 7106) SS BOND : bond 0.01061 / 0.71 ( 1) SS BOND : angle 1.82896 / 1.15 ( 2) hydrogen bonds : bond 0.05682 / 3.95 ( 186) hydrogen bonds : angle 4.68612 / 3.40 ( 423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.142 Fit side-chains REVERT: O 22 LYS cc_start: 0.7224 (mmmm) cc_final: 0.6705 (mtpt) REVERT: O 120 MET cc_start: 0.4991 (ppp) cc_final: 0.4631 (ppp) outliers start: 17 outliers final: 17 residues processed: 53 average time/residue: 0.0778 time to fit residues: 5.3128 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4591 r_free = 0.4591 target = 0.207272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185968 restraints weight = 8499.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.189547 restraints weight = 4602.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.191980 restraints weight = 2854.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.193583 restraints weight = 1954.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.194648 restraints weight = 1465.558| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4988 Z= 0.137 Angle : 0.553 8.513 7108 Z= 0.311 Chirality : 0.039 0.236 860 Planarity : 0.005 0.052 635 Dihedral : 20.634 133.291 1625 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.35 % Allowed : 26.09 % Favored : 69.57 % 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: -0.43 (0.41), residues: 408 helix: 3.19 (1.61), residues: 12 sheet: 0.33 (0.41), residues: 166 loop : -0.95 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 74 TYR 0.011 0.002 TYR P 96 PHE 0.019 0.002 PHE O 157 TRP 0.013 0.002 TRP Q 90 HIS 0.003 0.001 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 4987) covalent geometry : angle 0.55328 / 0.31 ( 7106) SS BOND : bond 0.00793 / 0.53 ( 1) SS BOND : angle 0.97320 / 0.57 ( 2) hydrogen bonds : bond 0.05197 / 3.65 ( 186) hydrogen bonds : angle 4.62280 / 3.33 ( 423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.167 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 49 average time/residue: 0.0661 time to fit residues: 4.2750 Evaluate side-chains 57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 88 GLN ** 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 = 0.4576 r_free = 0.4576 target = 0.205945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.184045 restraints weight = 8411.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.187791 restraints weight = 4476.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.190318 restraints weight = 2735.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.191940 restraints weight = 1855.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.192925 restraints weight = 1382.263| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4988 Z= 0.173 Angle : 0.605 9.144 7108 Z= 0.337 Chirality : 0.041 0.238 860 Planarity : 0.005 0.054 635 Dihedral : 20.700 133.564 1625 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.35 % Allowed : 25.80 % Favored : 69.86 % 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: -0.58 (0.41), residues: 408 helix: 3.12 (1.63), residues: 12 sheet: 0.18 (0.40), residues: 168 loop : -1.02 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 89 TYR 0.016 0.002 TYR O 139 PHE 0.021 0.002 PHE O 157 TRP 0.015 0.002 TRP Q 90 HIS 0.003 0.002 HIS O 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 4987) covalent geometry : angle 0.60412 / 0.34 ( 7106) SS BOND : bond 0.01090 / 0.73 ( 1) SS BOND : angle 1.74279 / 1.08 ( 2) hydrogen bonds : bond 0.05781 / 4.02 ( 186) hydrogen bonds : angle 4.68588 / 3.39 ( 423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.126 Fit side-chains REVERT: O 120 MET cc_start: 0.5204 (ppp) cc_final: 0.4900 (ppp) REVERT: P 115 MET cc_start: 0.5910 (mmt) cc_final: 0.5700 (mmt) outliers start: 15 outliers final: 13 residues processed: 52 average time/residue: 0.0733 time to fit residues: 5.0045 Evaluate side-chains 58 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 84 GLN ** Q 88 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 = 0.4578 r_free = 0.4578 target = 0.206050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.183990 restraints weight = 8390.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187825 restraints weight = 4413.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.190372 restraints weight = 2681.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.192036 restraints weight = 1818.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.193186 restraints weight = 1347.097| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4988 Z= 0.171 Angle : 0.613 9.888 7108 Z= 0.338 Chirality : 0.040 0.236 860 Planarity : 0.005 0.054 635 Dihedral : 20.735 132.716 1625 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.35 % Allowed : 24.93 % Favored : 70.72 % 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: -0.68 (0.41), residues: 408 helix: 3.02 (1.64), residues: 12 sheet: 0.09 (0.40), residues: 168 loop : -1.07 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 74 TYR 0.013 0.002 TYR O 139 PHE 0.020 0.002 PHE O 157 TRP 0.015 0.003 TRP Q 90 HIS 0.004 0.002 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 4987) covalent geometry : angle 0.61221 / 0.34 ( 7106) SS BOND : bond 0.00964 / 0.64 ( 1) SS BOND : angle 1.44479 / 0.88 ( 2) hydrogen bonds : bond 0.05756 / 3.98 ( 186) hydrogen bonds : angle 4.72441 / 3.39 ( 423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.46 seconds wall clock time: 17 minutes 23.69 seconds (1043.69 seconds total)