Starting phenix.real_space_refine on Fri Aug 22 22:00:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooa_17008/08_2025/8ooa_17008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooa_17008/08_2025/8ooa_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_17008/08_2025/8ooa_17008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooa_17008/08_2025/8ooa_17008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ooa_17008/08_2025/8ooa_17008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooa_17008/08_2025/8ooa_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-2.0-5787/lib/python3.9/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: 2.16, per 1000 atoms: 0.26 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: 0.73 Conformation dependent library (CDL) restraints added in 320.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.44 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: 1.54 Time building geometry restraints manager: 0.96 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=" C4' DG L 63 " pdb=" C3' DG L 63 " ideal model delta sigma weight residual 1.523 1.577 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.523 1.575 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C4' DG K 20 " pdb=" C3' DG K 20 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C4' DG L -5 " pdb=" C3' DG L -5 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C4' DC K 4 " pdb=" C3' DC K 4 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 9801 0.95 - 1.90: 1946 1.90 - 2.85: 705 2.85 - 3.80: 470 3.80 - 4.75: 49 Bond angle restraints: 12971 Sorted by residual: angle pdb=" O3' DC L -25 " pdb=" P DT L -24 " pdb=" O5' DT L -24 " ideal model delta sigma weight residual 104.00 99.62 4.38 1.50e+00 4.44e-01 8.54e+00 angle pdb=" C4' DC K 21 " pdb=" O4' DC K 21 " pdb=" C1' DC K 21 " ideal model delta sigma weight residual 109.70 105.34 4.36 1.50e+00 4.44e-01 8.45e+00 angle pdb=" O3' DG L 27 " pdb=" P DA L 28 " pdb=" O5' DA L 28 " ideal model delta sigma weight residual 104.00 99.89 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" O3' DC L -28 " pdb=" P DC L -27 " pdb=" O5' DC L -27 " ideal model delta sigma weight residual 104.00 99.93 4.07 1.50e+00 4.44e-01 7.35e+00 angle pdb=" O3' DA K -45 " pdb=" P DA K -44 " pdb=" O5' DA K -44 " ideal model delta sigma weight residual 104.00 100.01 3.99 1.50e+00 4.44e-01 7.09e+00 ... (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: 741 0.039 - 0.079: 516 0.079 - 0.118: 156 0.118 - 0.157: 51 0.157 - 0.196: 11 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=" C1' DT L 15 " pdb=" O4' DT L 15 " pdb=" C2' DT L 15 " pdb=" N1 DT L 15 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.05e-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 ... (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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.650 Find NCS groups from input model: 0.060 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.008 0.057 8965 Z= 0.378 Angle : 1.083 4.754 12971 Z= 0.589 Chirality : 0.057 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 aren 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 covalent geometry : bond 0.00812 ( 8965) covalent geometry : angle 1.08321 (12971) hydrogen bonds : bond 0.22375 ( 425) hydrogen bonds : angle 8.43492 ( 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 : 0.240 Fit side-chains revert: symmetry clash REVERT: N 57 VAL cc_start: 0.8072 (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: 0.1995 time to fit residues: 29.0751 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 : 0.234 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3729 r_free = 0.3729 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110285 restraints weight = 11147.607| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.71 r_work: 0.3352 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8965 Z= 0.182 Angle : 0.590 4.828 12971 Z= 0.357 Chirality : 0.036 0.134 1475 Planarity : 0.004 0.032 936 Dihedral : 32.273 90.757 2801 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.68 % Allowed : 6.55 % Favored : 92.78 % 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 aren not related in a simple way. whole: 1.20 (0.35), residues: 517 helix: 1.20 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.19 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 76 TYR 0.019 0.002 TYR N 88 PHE 0.016 0.002 PHE P 62 HIS 0.007 0.002 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8965) covalent geometry : angle 0.59021 (12971) hydrogen bonds : bond 0.04869 ( 425) hydrogen bonds : angle 3.50170 ( 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 99 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: N 91 LYS cc_start: 0.8061 (mttt) cc_final: 0.7551 (mmtt) REVERT: N 92 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6880 (mtp85) REVERT: P 68 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6683 (mt-10) REVERT: P 82 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7344 (mttp) REVERT: Q 58 THR cc_start: 0.7184 (p) cc_final: 0.6753 (p) REVERT: Q 109 LEU cc_start: 0.8371 (mt) cc_final: 0.8129 (mm) REVERT: R 25 ASN cc_start: 0.7731 (m-40) cc_final: 0.7446 (m110) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.1846 time to fit residues: 21.6477 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0000 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Q 68 GLN Q 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113357 restraints weight = 10883.155| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 0.70 r_work: 0.3396 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8965 Z= 0.150 Angle : 0.541 4.923 12971 Z= 0.329 Chirality : 0.033 0.137 1475 Planarity : 0.004 0.037 936 Dihedral : 31.567 92.237 2801 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.68 % Allowed : 7.90 % Favored : 91.42 % 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 aren not related in a simple way. whole: 2.18 (0.36), residues: 517 helix: 1.97 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.09 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 71 TYR 0.019 0.002 TYR N 88 PHE 0.019 0.002 PHE P 62 HIS 0.005 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8965) covalent geometry : angle 0.54138 (12971) hydrogen bonds : bond 0.03611 ( 425) hydrogen bonds : angle 3.10424 ( 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 98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: N 91 LYS cc_start: 0.8030 (mttt) cc_final: 0.7684 (mtpt) REVERT: N 92 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6869 (mtp85) REVERT: O 24 GLN cc_start: 0.8109 (mp10) cc_final: 0.7897 (mm-40) REVERT: P 82 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7383 (mttp) REVERT: Q 50 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7068 (mm-30) REVERT: Q 64 LYS cc_start: 0.7113 (mtmt) cc_final: 0.6728 (mtpt) REVERT: R 25 ASN cc_start: 0.7799 (m-40) cc_final: 0.7350 (m110) outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.1909 time to fit residues: 22.0424 Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN P 44 GLN Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107539 restraints weight = 11258.260| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 0.67 r_work: 0.3308 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8965 Z= 0.214 Angle : 0.617 5.262 12971 Z= 0.366 Chirality : 0.038 0.149 1475 Planarity : 0.005 0.043 936 Dihedral : 31.769 89.276 2801 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.13 % Allowed : 10.16 % Favored : 88.71 % 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 aren not related in a simple way. whole: 1.77 (0.35), residues: 517 helix: 1.62 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.05 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 128 TYR 0.046 0.003 TYR N 88 PHE 0.014 0.002 PHE R 100 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8965) covalent geometry : angle 0.61725 (12971) hydrogen bonds : bond 0.04490 ( 425) hydrogen bonds : angle 3.37524 ( 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: 5 poor density : 87 time to evaluate : 0.235 Fit side-chains REVERT: N 92 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6777 (mtp85) REVERT: R 25 ASN cc_start: 0.7822 (m-40) cc_final: 0.7387 (m110) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1715 time to fit residues: 18.8193 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN O 104 GLN P 44 GLN Q 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108384 restraints weight = 11153.222| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.70 r_work: 0.3317 rms_B_bonded: 1.90 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: 0.7336 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8965 Z= 0.172 Angle : 0.576 4.886 12971 Z= 0.347 Chirality : 0.035 0.145 1475 Planarity : 0.004 0.035 936 Dihedral : 31.634 89.727 2801 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 10.16 % 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 aren not related in a simple way. whole: 1.98 (0.36), residues: 517 helix: 1.79 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 53 TYR 0.063 0.003 TYR N 88 PHE 0.011 0.002 PHE P 62 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8965) covalent geometry : angle 0.57623 (12971) hydrogen bonds : bond 0.04093 ( 425) hydrogen bonds : angle 3.27119 ( 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 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: N 92 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6793 (mtp85) REVERT: P 82 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7375 (mttm) REVERT: R 25 ASN cc_start: 0.7815 (m-40) cc_final: 0.7383 (m110) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1783 time to fit residues: 19.0194 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 O residue 104 GLN Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 57 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: 2.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN P 44 GLN Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108981 restraints weight = 11147.453| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.66 r_work: 0.3335 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8965 Z= 0.180 Angle : 0.568 4.842 12971 Z= 0.341 Chirality : 0.035 0.145 1475 Planarity : 0.004 0.035 936 Dihedral : 31.312 89.942 2801 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 11.74 % 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 aren not related in a simple way. whole: 2.03 (0.36), residues: 517 helix: 1.86 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.14 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 53 TYR 0.060 0.002 TYR N 88 PHE 0.011 0.002 PHE R 100 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8965) covalent geometry : angle 0.56781 (12971) hydrogen bonds : bond 0.03904 ( 425) hydrogen bonds : angle 3.25606 ( 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 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.250 Fit side-chains REVERT: N 92 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6728 (mtp85) REVERT: P 82 LYS cc_start: 0.7782 (mtmm) cc_final: 0.7325 (mttm) REVERT: R 25 ASN cc_start: 0.7797 (m-40) cc_final: 0.7357 (m110) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.1730 time to fit residues: 19.0776 Evaluate side-chains 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 55 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 45 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 overall best weight: 0.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN N 27 GLN P 44 GLN P 64 ASN Q 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110908 restraints weight = 11144.657| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.66 r_work: 0.3363 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8965 Z= 0.143 Angle : 0.546 7.187 12971 Z= 0.330 Chirality : 0.033 0.142 1475 Planarity : 0.004 0.033 936 Dihedral : 31.255 91.369 2801 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.68 % Allowed : 12.64 % Favored : 86.68 % 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 aren not related in a simple way. whole: 2.46 (0.36), residues: 517 helix: 2.19 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.07 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 53 TYR 0.058 0.002 TYR N 88 PHE 0.015 0.002 PHE P 62 HIS 0.002 0.001 HIS P 79 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8965) covalent geometry : angle 0.54582 (12971) hydrogen bonds : bond 0.03578 ( 425) hydrogen bonds : angle 3.12240 ( 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 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: P 82 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7297 (mttm) REVERT: R 25 ASN cc_start: 0.7785 (m-40) cc_final: 0.7357 (m110) outliers start: 3 outliers final: 2 residues processed: 86 average time/residue: 0.1839 time to fit residues: 19.1986 Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU 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: 1.9990 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN N 27 GLN O 104 GLN P 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104852 restraints weight = 11223.064| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 0.73 r_work: 0.3268 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8965 Z= 0.272 Angle : 0.666 6.265 12971 Z= 0.392 Chirality : 0.040 0.165 1475 Planarity : 0.005 0.050 936 Dihedral : 31.784 87.925 2801 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.58 % Allowed : 11.96 % Favored : 86.46 % 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 aren not related in a simple way. whole: 1.50 (0.35), residues: 517 helix: 1.42 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.13 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 69 TYR 0.061 0.003 TYR N 88 PHE 0.013 0.002 PHE R 100 HIS 0.007 0.002 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 8965) covalent geometry : angle 0.66568 (12971) hydrogen bonds : bond 0.04917 ( 425) hydrogen bonds : angle 3.54859 ( 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 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.234 Fit side-chains REVERT: N 92 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6740 (mtp85) REVERT: R 25 ASN cc_start: 0.7799 (m-40) cc_final: 0.7577 (m-40) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.1632 time to fit residues: 17.2705 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 O residue 104 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN P 44 GLN Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108028 restraints weight = 11204.937| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.61 r_work: 0.3325 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8965 Z= 0.184 Angle : 0.590 6.361 12971 Z= 0.354 Chirality : 0.036 0.148 1475 Planarity : 0.005 0.034 936 Dihedral : 31.507 90.449 2801 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.13 % Allowed : 12.42 % Favored : 86.46 % 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 aren not related in a simple way. whole: 1.87 (0.36), residues: 517 helix: 1.73 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.13 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 53 TYR 0.059 0.003 TYR N 88 PHE 0.009 0.002 PHE R 100 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8965) covalent geometry : angle 0.59043 (12971) hydrogen bonds : bond 0.04145 ( 425) hydrogen bonds : angle 3.34816 ( 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 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.203 Fit side-chains REVERT: N 92 ARG cc_start: 0.7080 (mtp85) cc_final: 0.6734 (mtp85) REVERT: P 82 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7464 (mttm) REVERT: R 25 ASN cc_start: 0.7764 (m-40) cc_final: 0.7392 (m110) outliers start: 5 outliers final: 5 residues processed: 84 average time/residue: 0.1726 time to fit residues: 17.6423 Evaluate side-chains 83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 P residue 98 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106777 restraints weight = 11209.904| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.67 r_work: 0.3298 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8965 Z= 0.220 Angle : 0.614 6.314 12971 Z= 0.365 Chirality : 0.037 0.151 1475 Planarity : 0.005 0.036 936 Dihedral : 31.422 89.527 2801 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.13 % Allowed : 12.64 % 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 aren 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 : -0.24 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 49 TYR 0.056 0.003 TYR N 88 PHE 0.011 0.002 PHE R 100 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8965) covalent geometry : angle 0.61384 (12971) hydrogen bonds : bond 0.04388 ( 425) hydrogen bonds : angle 3.40383 ( 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 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.235 Fit side-chains REVERT: N 92 ARG cc_start: 0.7117 (mtp85) cc_final: 0.6795 (mtp85) REVERT: P 82 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7472 (mttm) REVERT: R 25 ASN cc_start: 0.7787 (m-40) cc_final: 0.7563 (m-40) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.1848 time to fit residues: 18.6374 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 P residue 98 LEU Chi-restraints excluded: chain Q residue 57 SER 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: 0.3980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN 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 = 0.124946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107537 restraints weight = 11122.779| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.70 r_work: 0.3306 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8965 Z= 0.173 Angle : 0.584 6.155 12971 Z= 0.352 Chirality : 0.035 0.148 1475 Planarity : 0.005 0.035 936 Dihedral : 31.386 90.742 2801 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.90 % Allowed : 12.87 % 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 aren not related in a simple way. whole: 1.94 (0.36), residues: 517 helix: 1.79 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.18 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 53 TYR 0.069 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 covalent geometry : bond 0.00378 ( 8965) covalent geometry : angle 0.58369 (12971) hydrogen bonds : bond 0.04117 ( 425) hydrogen bonds : angle 3.29576 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.15 seconds wall clock time: 42 minutes 42.76 seconds (2562.76 seconds total)