Starting phenix.real_space_refine on Thu Jul 2 09:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooa_17008/07_2026/8ooa_17008.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 204 5.49 5 S 12 5.16 5 C 4638 2.51 5 N 1589 2.21 5 O 1962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8405 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2086 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "L" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2096 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 1.67, per 1000 atoms: 0.20 Number of scatterers: 8405 At special positions: 0 Unit cell: (114.258, 115.902, 77.268, 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 204 15.00 O 1962 8.00 N 1589 7.00 C 4638 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: 0.67 Conformation dependent library (CDL) restraints added in 236.9 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 74.3% alpha, 3.0% beta 58 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.267A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 113 removed outlier: 3.905A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.645A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 47 through 76 removed outlier: 4.178A pdb=" N TYR N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU N 52 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 43 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 122 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.209A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.507A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.529A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.639A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.671A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.220A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.523A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.382A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 118 through 119 284 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 190 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.90 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: 1955 1.34 - 1.45: 2579 1.45 - 1.57: 4002 1.57 - 1.69: 409 1.69 - 1.81: 20 Bond restraints: 8965 Sorted by residual: bond pdb=" C5' DG K 26 " pdb=" C4' DG K 26 " ideal model delta sigma weight residual 1.512 1.562 -0.050 7.00e-03 2.04e+04 5.01e+01 bond pdb=" C5' DC K -56 " pdb=" C4' DC K -56 " ideal model delta sigma weight residual 1.512 1.555 -0.043 7.00e-03 2.04e+04 3.74e+01 bond pdb=" C4' DG L 63 " pdb=" C3' DG L 63 " ideal model delta sigma weight residual 1.529 1.577 -0.048 1.00e-02 1.00e+04 2.26e+01 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.529 1.575 -0.046 1.00e-02 1.00e+04 2.13e+01 bond pdb=" C3' DC K -62 " pdb=" C2' DC K -62 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.90e+01 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 10089 0.95 - 1.90: 1676 1.90 - 2.86: 654 2.86 - 3.81: 498 3.81 - 4.76: 54 Bond angle restraints: 12971 Sorted by residual: angle pdb=" C4' DC K 21 " pdb=" O4' DC K 21 " pdb=" C1' DC K 21 " ideal model delta sigma weight residual 110.10 105.34 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" O5' DG K 26 " pdb=" C5' DG K 26 " pdb=" C4' DG K 26 " ideal model delta sigma weight residual 109.40 113.02 -3.62 8.00e-01 1.56e+00 2.05e+01 angle pdb=" C4' DC K -62 " pdb=" O4' DC K -62 " pdb=" C1' DC K -62 " ideal model delta sigma weight residual 110.10 105.88 4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" C4' DG K 25 " pdb=" O4' DG K 25 " pdb=" C1' DG K 25 " ideal model delta sigma weight residual 110.10 105.89 4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" O5' DC K -46 " pdb=" C5' DC K -46 " pdb=" C4' DC K -46 " ideal model delta sigma weight residual 109.40 112.77 -3.37 8.00e-01 1.56e+00 1.77e+01 ... (remaining 12966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3198 17.66 - 35.31: 630 35.31 - 52.97: 794 52.97 - 70.62: 212 70.62 - 88.28: 25 Dihedral angle restraints: 4859 sinusoidal: 3327 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ILE M 112 " pdb=" C ILE M 112 " pdb=" N HIS M 113 " pdb=" CA HIS M 113 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ASP Q 81 " pdb=" C ASP Q 81 " pdb=" N LEU Q 82 " pdb=" CA LEU Q 82 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLY N 28 " pdb=" C GLY N 28 " pdb=" N ILE N 29 " pdb=" CA ILE N 29 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 660 0.039 - 0.079: 577 0.079 - 0.118: 194 0.118 - 0.157: 38 0.157 - 0.196: 6 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ILE O 79 " pdb=" N ILE O 79 " pdb=" C ILE O 79 " pdb=" CB ILE O 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C3' DC L -20 " pdb=" C4' DC L -20 " pdb=" O3' DC L -20 " pdb=" C2' DC L -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 1472 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 92 " -0.324 9.50e-02 1.11e+02 1.46e-01 1.58e+01 pdb=" NE ARG N 92 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG N 92 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG N 92 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG N 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " 0.003 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR Q 41 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 83 " -0.240 9.50e-02 1.11e+02 1.08e-01 8.70e+00 pdb=" NE ARG M 83 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG M 83 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG M 83 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG M 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1742 2.82 - 3.34: 7553 3.34 - 3.86: 16370 3.86 - 4.38: 20627 4.38 - 4.90: 28006 Nonbonded interactions: 74298 Sorted by model distance: nonbonded pdb=" OH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 2.299 3.040 nonbonded pdb=" OD2 ASP M 106 " pdb=" NH1 ARG M 131 " model vdw 2.377 3.120 nonbonded pdb=" OP1 DG L 8 " pdb=" N ILE N 46 " model vdw 2.398 3.120 nonbonded pdb=" OP1 DA L 28 " pdb=" N LYS N 79 " model vdw 2.412 3.120 nonbonded pdb=" OD2 ASP P 65 " pdb=" OH TYR R 98 " model vdw 2.425 3.040 ... (remaining 74293 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 Found NCS groups: ncs_group { reference = (chain 'N' and resid 23 through 95) selection = (chain 'R' and resid 23 through 95) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.070 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.007 0.062 8965 Z= 0.643 Angle : 1.062 4.761 12971 Z= 0.647 Chirality : 0.058 0.196 1475 Planarity : 0.012 0.146 936 Dihedral : 27.962 88.276 3869 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.30), residues: 517 helix: -1.41 (0.21), residues: 388 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG N 92 TYR 0.035 0.006 TYR Q 41 PHE 0.026 0.002 PHE R 100 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.64 ( 8965) covalent geometry : angle 1.06227 / 0.65 (12971) hydrogen bonds : bond 0.22375 / 24.51 ( 425) hydrogen bonds : angle 8.43492 / 10.68 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: N 57 VAL cc_start: 0.8071 (t) cc_final: 0.7789 (m) REVERT: N 91 LYS cc_start: 0.8304 (mttt) cc_final: 0.7853 (mtpt) REVERT: O 74 LYS cc_start: 0.7891 (mttt) cc_final: 0.7667 (mptt) REVERT: P 32 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5638 (pt0) REVERT: P 44 GLN cc_start: 0.7192 (mt0) cc_final: 0.6991 (mt0) REVERT: Q 58 THR cc_start: 0.7089 (p) cc_final: 0.6852 (p) REVERT: Q 64 LYS cc_start: 0.7827 (mttt) cc_final: 0.7426 (mtpt) REVERT: Q 68 GLN cc_start: 0.8021 (mt0) cc_final: 0.7814 (mt0) REVERT: R 25 ASN cc_start: 0.7507 (m-40) cc_final: 0.7123 (m110) REVERT: R 57 VAL cc_start: 0.8440 (t) cc_final: 0.8096 (m) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1678 time to fit residues: 24.6621 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 125 GLN O 104 GLN P 60 ASN P 64 ASN P 79 HIS P 81 ASN R 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110143 restraints weight = 11163.690| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 0.67 r_work: 0.3352 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8965 Z= 0.183 Angle : 0.742 8.140 12971 Z= 0.420 Chirality : 0.052 0.228 1475 Planarity : 0.005 0.048 936 Dihedral : 32.620 98.106 2801 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.90 % Allowed : 6.55 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.34), residues: 517 helix: 0.81 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.31 (0.46), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 63 TYR 0.043 0.003 TYR N 88 PHE 0.017 0.003 PHE R 100 HIS 0.005 0.001 HIS P 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 ( 8965) covalent geometry : angle 0.74244 / 0.42 (12971) hydrogen bonds : bond 0.06918 / 7.84 ( 425) hydrogen bonds : angle 3.90709 / 5.19 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: P 68 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6731 (mt-10) REVERT: P 82 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7401 (mttp) REVERT: Q 58 THR cc_start: 0.7157 (p) cc_final: 0.6727 (p) REVERT: Q 64 LYS cc_start: 0.7514 (mttt) cc_final: 0.7066 (mtpt) REVERT: R 25 ASN cc_start: 0.7689 (m-40) cc_final: 0.7426 (m110) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.1494 time to fit residues: 17.2331 Evaluate side-chains 81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN Q 39 HIS Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105426 restraints weight = 11097.650| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.76 r_work: 0.3274 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8965 Z= 0.222 Angle : 0.752 7.403 12971 Z= 0.421 Chirality : 0.053 0.236 1475 Planarity : 0.006 0.057 936 Dihedral : 32.806 95.694 2801 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.90 % Allowed : 8.35 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.34), residues: 517 helix: 0.67 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.36 (0.46), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 128 TYR 0.042 0.004 TYR N 88 PHE 0.015 0.003 PHE R 100 HIS 0.009 0.003 HIS Q 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 ( 8965) covalent geometry : angle 0.75151 / 0.42 (12971) hydrogen bonds : bond 0.05967 / 6.69 ( 425) hydrogen bonds : angle 3.76972 / 5.05 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: N 92 ARG cc_start: 0.7257 (mtp85) cc_final: 0.7022 (mtp85) REVERT: Q 64 LYS cc_start: 0.7478 (mttt) cc_final: 0.7098 (mtpt) REVERT: R 25 ASN cc_start: 0.7776 (m-40) cc_final: 0.7454 (m110) outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.1603 time to fit residues: 17.2042 Evaluate side-chains 83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104753 restraints weight = 11337.791| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.72 r_work: 0.3266 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8965 Z= 0.223 Angle : 0.741 7.272 12971 Z= 0.413 Chirality : 0.052 0.216 1475 Planarity : 0.006 0.046 936 Dihedral : 32.653 101.331 2801 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 9.93 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.34), residues: 517 helix: 0.75 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -0.54 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 78 TYR 0.050 0.003 TYR N 88 PHE 0.014 0.003 PHE R 100 HIS 0.005 0.002 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 ( 8965) covalent geometry : angle 0.74124 / 0.41 (12971) hydrogen bonds : bond 0.05417 / 6.06 ( 425) hydrogen bonds : angle 3.72416 / 4.96 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: M 106 ASP cc_start: 0.6766 (m-30) cc_final: 0.6558 (m-30) REVERT: N 92 ARG cc_start: 0.7156 (mtp85) cc_final: 0.6914 (mtp85) REVERT: Q 64 LYS cc_start: 0.7454 (mttt) cc_final: 0.7089 (mtpt) REVERT: R 25 ASN cc_start: 0.7797 (m-40) cc_final: 0.7484 (m110) outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 0.1433 time to fit residues: 15.6095 Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN ** P 64 ASN ** 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 = 0.3686 r_free = 0.3686 target = 0.125013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107033 restraints weight = 11224.654| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.71 r_work: 0.3298 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8965 Z= 0.161 Angle : 0.657 7.862 12971 Z= 0.374 Chirality : 0.047 0.230 1475 Planarity : 0.005 0.034 936 Dihedral : 32.381 107.771 2801 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.58 % Allowed : 12.19 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.35), residues: 517 helix: 1.28 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.52 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 69 TYR 0.061 0.003 TYR N 88 PHE 0.013 0.002 PHE P 62 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 8965) covalent geometry : angle 0.65703 / 0.37 (12971) hydrogen bonds : bond 0.04577 / 5.07 ( 425) hydrogen bonds : angle 3.48932 / 4.66 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.131 Fit side-chains REVERT: M 83 ARG cc_start: 0.7541 (mmt90) cc_final: 0.7291 (mtt180) REVERT: N 92 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6823 (mtp85) REVERT: P 73 GLU cc_start: 0.7200 (tp30) cc_final: 0.6991 (tp30) REVERT: Q 64 LYS cc_start: 0.7387 (mttt) cc_final: 0.7011 (mtpt) REVERT: R 25 ASN cc_start: 0.7759 (m-40) cc_final: 0.7430 (m110) outliers start: 7 outliers final: 4 residues processed: 86 average time/residue: 0.1443 time to fit residues: 15.1216 Evaluate side-chains 83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 57 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 68 GLN ** P 64 ASN ** 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 = 0.3705 r_free = 0.3705 target = 0.126482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108643 restraints weight = 11107.144| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.69 r_work: 0.3327 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8965 Z= 0.134 Angle : 0.611 6.021 12971 Z= 0.355 Chirality : 0.044 0.191 1475 Planarity : 0.004 0.032 936 Dihedral : 32.157 110.236 2801 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.48 % Allowed : 12.87 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.36), residues: 517 helix: 1.76 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.37 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 20 TYR 0.062 0.002 TYR N 88 PHE 0.014 0.002 PHE P 62 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 8965) covalent geometry : angle 0.61062 / 0.36 (12971) hydrogen bonds : bond 0.04139 / 4.61 ( 425) hydrogen bonds : angle 3.31312 / 4.44 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.208 Fit side-chains REVERT: M 83 ARG cc_start: 0.7493 (mmt90) cc_final: 0.7257 (mtt180) REVERT: N 92 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6753 (mtp85) REVERT: O 24 GLN cc_start: 0.8336 (mp10) cc_final: 0.8043 (mm-40) REVERT: P 82 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7452 (mttm) REVERT: Q 64 LYS cc_start: 0.7323 (mttt) cc_final: 0.6958 (mtpt) REVERT: R 25 ASN cc_start: 0.7766 (m-40) cc_final: 0.7446 (m110) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.1385 time to fit residues: 15.3460 Evaluate side-chains 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.2980 chunk 43 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN P 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108705 restraints weight = 11189.807| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.70 r_work: 0.3325 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8965 Z= 0.142 Angle : 0.599 5.657 12971 Z= 0.349 Chirality : 0.044 0.196 1475 Planarity : 0.004 0.033 936 Dihedral : 31.963 111.539 2801 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.48 % Allowed : 12.64 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.36), residues: 517 helix: 1.89 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.21 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 20 TYR 0.048 0.002 TYR N 88 PHE 0.012 0.002 PHE Q 67 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 8965) covalent geometry : angle 0.59945 / 0.35 (12971) hydrogen bonds : bond 0.04009 / 4.48 ( 425) hydrogen bonds : angle 3.25771 / 4.34 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.218 Fit side-chains REVERT: N 92 ARG cc_start: 0.7125 (mtp85) cc_final: 0.6805 (mtp85) REVERT: O 24 GLN cc_start: 0.8345 (mp10) cc_final: 0.8084 (mm-40) REVERT: P 82 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7384 (mttm) REVERT: Q 64 LYS cc_start: 0.7345 (mttt) cc_final: 0.6977 (mtpt) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.1518 time to fit residues: 16.3295 Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106539 restraints weight = 11113.599| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.70 r_work: 0.3295 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8965 Z= 0.176 Angle : 0.658 6.165 12971 Z= 0.373 Chirality : 0.047 0.211 1475 Planarity : 0.005 0.033 936 Dihedral : 32.083 112.468 2801 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.48 % Allowed : 14.00 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.35), residues: 517 helix: 1.53 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.23 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 20 TYR 0.069 0.003 TYR N 88 PHE 0.010 0.002 PHE R 61 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 8965) covalent geometry : angle 0.65844 / 0.37 (12971) hydrogen bonds : bond 0.04545 / 5.07 ( 425) hydrogen bonds : angle 3.44137 / 4.56 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.213 Fit side-chains REVERT: N 92 ARG cc_start: 0.7141 (mtp85) cc_final: 0.6844 (mtp85) REVERT: Q 64 LYS cc_start: 0.7401 (mttt) cc_final: 0.7042 (mtpt) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.1578 time to fit residues: 16.4852 Evaluate side-chains 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 93 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107225 restraints weight = 11240.222| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.70 r_work: 0.3305 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8965 Z= 0.149 Angle : 0.633 6.042 12971 Z= 0.362 Chirality : 0.046 0.209 1475 Planarity : 0.005 0.034 936 Dihedral : 32.049 113.409 2801 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.03 % Allowed : 13.77 % Favored : 84.20 % 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: 1.79 (0.35), residues: 517 helix: 1.68 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.19 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 20 TYR 0.066 0.003 TYR N 88 PHE 0.010 0.002 PHE R 100 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 ( 8965) covalent geometry : angle 0.63342 / 0.36 (12971) hydrogen bonds : bond 0.04281 / 4.76 ( 425) hydrogen bonds : angle 3.34884 / 4.47 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.230 Fit side-chains REVERT: N 92 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6793 (mtp85) REVERT: P 82 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7438 (mttm) REVERT: Q 64 LYS cc_start: 0.7394 (mttt) cc_final: 0.7024 (mtpt) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.1581 time to fit residues: 16.1057 Evaluate side-chains 86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 11 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.0030 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107996 restraints weight = 11178.468| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.70 r_work: 0.3317 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8965 Z= 0.136 Angle : 0.615 6.750 12971 Z= 0.354 Chirality : 0.045 0.204 1475 Planarity : 0.004 0.033 936 Dihedral : 31.972 114.910 2801 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 13.77 % Favored : 84.20 % 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: 2.05 (0.36), residues: 517 helix: 1.87 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.11 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 129 TYR 0.059 0.002 TYR N 88 PHE 0.011 0.002 PHE P 62 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 ( 8965) covalent geometry : angle 0.61522 / 0.35 (12971) hydrogen bonds : bond 0.04054 / 4.52 ( 425) hydrogen bonds : angle 3.29085 / 4.39 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.227 Fit side-chains REVERT: M 90 MET cc_start: 0.7201 (mmm) cc_final: 0.6915 (mmt) REVERT: N 92 ARG cc_start: 0.7106 (mtp85) cc_final: 0.6778 (mtp85) REVERT: P 82 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7437 (mttm) REVERT: Q 64 LYS cc_start: 0.7342 (mttt) cc_final: 0.6976 (mtpt) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.1375 time to fit residues: 13.8719 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 63 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108256 restraints weight = 11165.441| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 0.69 r_work: 0.3321 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8965 Z= 0.135 Angle : 0.606 5.780 12971 Z= 0.351 Chirality : 0.044 0.201 1475 Planarity : 0.004 0.033 936 Dihedral : 31.917 115.768 2801 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 13.77 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.36), residues: 517 helix: 1.91 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.10 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 20 TYR 0.063 0.002 TYR N 88 PHE 0.011 0.002 PHE P 67 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 ( 8965) covalent geometry : angle 0.60643 / 0.35 (12971) hydrogen bonds : bond 0.04007 / 4.46 ( 425) hydrogen bonds : angle 3.26234 / 4.36 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.79 seconds wall clock time: 36 minutes 32.07 seconds (2192.07 seconds total)