Starting phenix.real_space_refine on Fri Jul 3 01:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2026/8jld_36393.map" } resolution = 2.48 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= 0.006 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 10 5.16 5 C 6540 2.51 5 N 2221 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.08, per 1000 atoms: 0.18 Number of scatterers: 11844 At special positions: 0 Unit cell: (118.72, 110.24, 116.6, 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 10 16.00 P 289 15.00 O 2784 8.00 N 2221 7.00 C 6540 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: 0.93 Conformation dependent library (CDL) restraints added in 263.5 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.005A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.452A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.063A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.475A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.051A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.181A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.492A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.042A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.240A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.30 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: 2608 1.34 - 1.46: 4027 1.46 - 1.58: 5413 1.58 - 1.70: 577 1.70 - 1.82: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.53e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.20e+01 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 16704 1.54 - 3.09: 1474 3.09 - 4.63: 127 4.63 - 6.17: 10 6.17 - 7.72: 6 Bond angle restraints: 18321 Sorted by residual: angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 112.05 -4.05 7.00e-01 2.04e+00 3.35e+01 angle pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 109.40 113.86 -4.46 8.00e-01 1.56e+00 3.10e+01 angle pdb=" O5' DA I -45 " pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 109.40 113.68 -4.28 8.00e-01 1.56e+00 2.86e+01 angle pdb=" O4' DA I -45 " pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 4330 21.29 - 42.58: 1362 42.58 - 63.88: 1107 63.88 - 85.17: 46 85.17 - 106.46: 4 Dihedral angle restraints: 6849 sinusoidal: 4697 harmonic: 2152 Sorted by residual: dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 60.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual 90.00 42.05 47.95 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.79 44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1191 0.033 - 0.067: 617 0.067 - 0.100: 227 0.100 - 0.133: 39 0.133 - 0.166: 9 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA GLU G 64 " pdb=" N GLU G 64 " pdb=" C GLU G 64 " pdb=" CB GLU G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ARG E 63 " pdb=" N ARG E 63 " pdb=" C ARG E 63 " pdb=" CB ARG E 63 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG A 129 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 95 " 0.422 9.50e-02 1.11e+02 1.89e-01 2.19e+01 pdb=" NE ARG B 95 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 95 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 95 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 95 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " 0.016 2.00e-02 2.50e+03 1.71e-02 6.58e+00 pdb=" N1 DC J 19 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.004 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 7925 3.12 - 3.72: 20865 3.72 - 4.31: 30867 4.31 - 4.90: 43915 Nonbonded interactions: 103591 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 1.941 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.114 2.496 nonbonded pdb=" NH1 ARG C 11 " pdb=" O2 DT I -42 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE2 GLU H 71 " model vdw 2.297 3.040 ... (remaining 103586 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 : 0.006 0.036 12645 Z= 0.534 Angle : 0.858 7.717 18321 Z= 0.751 Chirality : 0.043 0.166 2083 Planarity : 0.014 0.424 1316 Dihedral : 29.740 106.461 5465 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 17.37 % Favored : 82.31 % 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: 0.65 (0.27), residues: 730 helix: 0.79 (0.20), residues: 538 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 131 TYR 0.011 0.002 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.53 (12645) covalent geometry : angle 0.85766 / 0.75 (18321) hydrogen bonds : bond 0.07192 / 4.74 ( 781) hydrogen bonds : angle 3.35582 / 2.53 ( 1948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.298 Fit side-chains REVERT: G 73 ASN cc_start: 0.8425 (t0) cc_final: 0.8170 (t0) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.9175 time to fit residues: 156.9709 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN F 93 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090565 restraints weight = 18258.600| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.98 r_work: 0.3193 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12645 Z= 0.140 Angle : 0.638 6.537 18321 Z= 0.376 Chirality : 0.047 0.234 2083 Planarity : 0.005 0.054 1316 Dihedral : 31.815 107.685 4005 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.11 % Allowed : 18.02 % Favored : 79.87 % 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: 3.27 (0.31), residues: 730 helix: 2.92 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.008 0.001 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (12645) covalent geometry : angle 0.63770 / 0.38 (18321) hydrogen bonds : bond 0.05250 / 3.60 ( 781) hydrogen bonds : angle 2.90575 / 2.19 ( 1948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.299 Fit side-chains REVERT: A 129 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7916 (tpt90) REVERT: C 11 ARG cc_start: 0.8104 (pmm-80) cc_final: 0.7783 (mtm-85) REVERT: C 13 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8554 (mmmt) REVERT: C 73 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8002 (t160) REVERT: D 76 GLU cc_start: 0.8338 (tp30) cc_final: 0.8095 (tp30) REVERT: E 63 ARG cc_start: 0.8477 (mmp80) cc_final: 0.8238 (mmp80) REVERT: F 84 MET cc_start: 0.8796 (mmm) cc_final: 0.8549 (mmp) REVERT: F 92 ARG cc_start: 0.8998 (ptm-80) cc_final: 0.8774 (ptm-80) REVERT: G 73 ASN cc_start: 0.8386 (t0) cc_final: 0.8118 (t0) outliers start: 13 outliers final: 7 residues processed: 168 average time/residue: 0.8757 time to fit residues: 154.7905 Evaluate side-chains 172 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088725 restraints weight = 18388.513| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.98 r_work: 0.3156 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12645 Z= 0.160 Angle : 0.615 6.366 18321 Z= 0.366 Chirality : 0.046 0.220 2083 Planarity : 0.004 0.040 1316 Dihedral : 31.522 109.728 4003 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.27 % Allowed : 18.67 % Favored : 79.06 % 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: 3.48 (0.31), residues: 730 helix: 3.09 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.014 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (12645) covalent geometry : angle 0.61505 / 0.37 (18321) hydrogen bonds : bond 0.05217 / 3.54 ( 781) hydrogen bonds : angle 2.83542 / 2.14 ( 1948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.320 Fit side-chains REVERT: B 35 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8289 (mtp85) REVERT: B 93 GLN cc_start: 0.8421 (mt0) cc_final: 0.8064 (mp10) REVERT: C 13 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8574 (mmmt) REVERT: C 73 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8096 (t160) REVERT: C 77 ARG cc_start: 0.9126 (mtm-85) cc_final: 0.8883 (mtt90) REVERT: E 63 ARG cc_start: 0.8459 (mmp80) cc_final: 0.8188 (mmp80) REVERT: E 129 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7931 (ttp80) REVERT: F 68 ASP cc_start: 0.8562 (m-30) cc_final: 0.8337 (m-30) REVERT: F 93 GLN cc_start: 0.8476 (mt0) cc_final: 0.8242 (mt0) REVERT: G 73 ASN cc_start: 0.8453 (t0) cc_final: 0.8159 (t0) REVERT: G 91 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.3424 (tp30) outliers start: 14 outliers final: 10 residues processed: 166 average time/residue: 0.8369 time to fit residues: 146.2849 Evaluate side-chains 173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0040 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN D 84 ASN E 76 GLN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083547 restraints weight = 18495.637| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.01 r_work: 0.3067 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12645 Z= 0.251 Angle : 0.732 7.927 18321 Z= 0.412 Chirality : 0.054 0.234 2083 Planarity : 0.005 0.040 1316 Dihedral : 31.362 113.834 4003 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.57 % Allowed : 17.53 % Favored : 78.90 % 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: 2.85 (0.30), residues: 730 helix: 2.63 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.022 0.003 TYR D 83 PHE 0.011 0.002 PHE A 67 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 (12645) covalent geometry : angle 0.73151 / 0.41 (18321) hydrogen bonds : bond 0.06563 / 4.42 ( 781) hydrogen bonds : angle 3.06727 / 2.31 ( 1948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8260 (mtt90) REVERT: A 129 ARG cc_start: 0.8340 (mmm160) cc_final: 0.7826 (tpt90) REVERT: B 35 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8263 (mtp85) REVERT: B 93 GLN cc_start: 0.8416 (mt0) cc_final: 0.8022 (mp10) REVERT: C 11 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7840 (ptm-80) REVERT: C 73 ASN cc_start: 0.8553 (t0) cc_final: 0.8236 (t160) REVERT: C 91 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: C 94 ASN cc_start: 0.8826 (t0) cc_final: 0.8542 (t0) REVERT: C 99 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: E 83 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7931 (mtm180) REVERT: F 93 GLN cc_start: 0.8610 (mt0) cc_final: 0.8342 (mt0) REVERT: G 73 ASN cc_start: 0.8514 (t0) cc_final: 0.8258 (t0) REVERT: G 91 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.3742 (tp30) outliers start: 22 outliers final: 9 residues processed: 176 average time/residue: 0.8457 time to fit residues: 156.6550 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 64 ASN E 76 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085496 restraints weight = 18300.184| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.98 r_work: 0.3098 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12645 Z= 0.143 Angle : 0.664 9.396 18321 Z= 0.382 Chirality : 0.050 0.229 2083 Planarity : 0.004 0.033 1316 Dihedral : 31.355 116.713 4003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.11 % Allowed : 19.32 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.30), residues: 730 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 35 TYR 0.013 0.001 TYR D 83 PHE 0.009 0.001 PHE D 70 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12645) covalent geometry : angle 0.66433 / 0.38 (18321) hydrogen bonds : bond 0.05642 / 3.84 ( 781) hydrogen bonds : angle 2.90446 / 2.19 ( 1948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7795 (tpt90) REVERT: B 35 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8310 (mtp85) REVERT: B 93 GLN cc_start: 0.8395 (mt0) cc_final: 0.7991 (mm-40) REVERT: C 73 ASN cc_start: 0.8490 (t0) cc_final: 0.8147 (t160) REVERT: G 73 ASN cc_start: 0.8473 (t0) cc_final: 0.8209 (t0) REVERT: G 91 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.3714 (tp30) outliers start: 13 outliers final: 5 residues processed: 165 average time/residue: 0.8821 time to fit residues: 153.1129 Evaluate side-chains 164 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083473 restraints weight = 18471.052| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.99 r_work: 0.3067 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12645 Z= 0.249 Angle : 0.706 7.489 18321 Z= 0.401 Chirality : 0.053 0.265 2083 Planarity : 0.005 0.037 1316 Dihedral : 31.214 120.529 4003 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.44 % Allowed : 19.64 % Favored : 77.92 % 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: 2.83 (0.30), residues: 730 helix: 2.62 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 92 TYR 0.017 0.002 TYR D 83 PHE 0.011 0.002 PHE A 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (12645) covalent geometry : angle 0.70629 / 0.40 (18321) hydrogen bonds : bond 0.06356 / 4.30 ( 781) hydrogen bonds : angle 2.99502 / 2.26 ( 1948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.9114 (m) cc_final: 0.8911 (m) REVERT: A 129 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7800 (tpt90) REVERT: B 35 ARG cc_start: 0.8623 (mtp85) cc_final: 0.8302 (mtp85) REVERT: B 93 GLN cc_start: 0.8476 (mt0) cc_final: 0.8078 (mm-40) REVERT: C 11 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7532 (pmm-80) REVERT: C 73 ASN cc_start: 0.8566 (t0) cc_final: 0.8223 (t160) REVERT: C 91 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.5765 (mp0) REVERT: C 94 ASN cc_start: 0.8820 (t0) cc_final: 0.8517 (t0) REVERT: C 99 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (mtm110) REVERT: E 83 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: G 73 ASN cc_start: 0.8511 (t0) cc_final: 0.8256 (t0) REVERT: G 91 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.3621 (tp30) outliers start: 15 outliers final: 7 residues processed: 166 average time/residue: 0.9331 time to fit residues: 162.7958 Evaluate side-chains 171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN F 27 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084816 restraints weight = 18315.345| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.97 r_work: 0.3091 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12645 Z= 0.147 Angle : 0.669 9.416 18321 Z= 0.385 Chirality : 0.050 0.257 2083 Planarity : 0.004 0.038 1316 Dihedral : 31.231 121.754 4003 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.27 % Allowed : 19.16 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.30), residues: 730 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.26 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.019 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (12645) covalent geometry : angle 0.66950 / 0.39 (18321) hydrogen bonds : bond 0.05721 / 3.89 ( 781) hydrogen bonds : angle 2.90910 / 2.19 ( 1948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.9089 (m) cc_final: 0.8887 (m) REVERT: A 129 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7789 (tpt90) REVERT: B 35 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8321 (mtp85) REVERT: B 93 GLN cc_start: 0.8427 (mt0) cc_final: 0.8026 (mm-40) REVERT: C 11 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7482 (pmm-80) REVERT: C 73 ASN cc_start: 0.8534 (t0) cc_final: 0.8199 (t160) REVERT: C 91 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: C 99 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7600 (mtm110) REVERT: G 73 ASN cc_start: 0.8460 (t0) cc_final: 0.8201 (t0) REVERT: G 91 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.3629 (tp30) outliers start: 14 outliers final: 8 residues processed: 166 average time/residue: 0.9269 time to fit residues: 161.8125 Evaluate side-chains 170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN F 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083574 restraints weight = 18505.065| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.99 r_work: 0.3067 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12645 Z= 0.230 Angle : 0.697 7.711 18321 Z= 0.396 Chirality : 0.051 0.261 2083 Planarity : 0.005 0.037 1316 Dihedral : 31.149 124.453 4003 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.57 % Allowed : 18.83 % Favored : 77.60 % 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: 2.89 (0.30), residues: 730 helix: 2.67 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.020 0.002 TYR D 83 PHE 0.011 0.002 PHE A 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (12645) covalent geometry : angle 0.69673 / 0.40 (18321) hydrogen bonds : bond 0.06122 / 4.15 ( 781) hydrogen bonds : angle 2.94526 / 2.22 ( 1948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8267 (mtt90) REVERT: A 129 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7780 (tpt90) REVERT: B 35 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8305 (mtp85) REVERT: B 93 GLN cc_start: 0.8475 (mt0) cc_final: 0.8184 (mm-40) REVERT: C 11 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7527 (pmm-80) REVERT: C 73 ASN cc_start: 0.8573 (t0) cc_final: 0.8232 (t160) REVERT: C 91 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.5788 (mp0) REVERT: C 94 ASN cc_start: 0.8810 (t0) cc_final: 0.8500 (t160) REVERT: C 99 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7635 (mtm110) REVERT: F 93 GLN cc_start: 0.8564 (mt0) cc_final: 0.8328 (mt0) REVERT: G 73 ASN cc_start: 0.8505 (t0) cc_final: 0.8248 (t0) REVERT: G 91 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.3613 (tp30) outliers start: 22 outliers final: 9 residues processed: 170 average time/residue: 0.9459 time to fit residues: 168.8666 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN F 27 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084920 restraints weight = 18181.662| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.96 r_work: 0.3095 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12645 Z= 0.144 Angle : 0.661 8.915 18321 Z= 0.381 Chirality : 0.050 0.248 2083 Planarity : 0.004 0.034 1316 Dihedral : 31.157 126.353 4003 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.44 % Allowed : 19.64 % Favored : 77.92 % 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: 3.09 (0.30), residues: 730 helix: 2.83 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.023 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12645) covalent geometry : angle 0.66091 / 0.38 (18321) hydrogen bonds : bond 0.05623 / 3.84 ( 781) hydrogen bonds : angle 2.87636 / 2.16 ( 1948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7776 (tpt90) REVERT: B 35 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8316 (mtp85) REVERT: B 93 GLN cc_start: 0.8429 (mt0) cc_final: 0.8131 (mm-40) REVERT: C 11 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7470 (pmm-80) REVERT: C 73 ASN cc_start: 0.8539 (t0) cc_final: 0.8199 (t160) REVERT: C 91 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5705 (mp0) REVERT: C 99 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7607 (mtm110) REVERT: G 73 ASN cc_start: 0.8466 (t0) cc_final: 0.8205 (t0) REVERT: G 91 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.3584 (tp30) outliers start: 15 outliers final: 8 residues processed: 171 average time/residue: 0.9176 time to fit residues: 165.1140 Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 0.0370 chunk 35 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084798 restraints weight = 18419.655| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.97 r_work: 0.3092 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12645 Z= 0.180 Angle : 0.658 8.105 18321 Z= 0.379 Chirality : 0.049 0.248 2083 Planarity : 0.004 0.035 1316 Dihedral : 31.123 129.490 4003 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.27 % Allowed : 20.45 % Favored : 77.27 % 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: 3.07 (0.30), residues: 730 helix: 2.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.022 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (12645) covalent geometry : angle 0.65847 / 0.38 (18321) hydrogen bonds : bond 0.05636 / 3.85 ( 781) hydrogen bonds : angle 2.84443 / 2.14 ( 1948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7771 (tpt90) REVERT: B 35 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8327 (mtp85) REVERT: B 93 GLN cc_start: 0.8447 (mt0) cc_final: 0.8144 (mm-40) REVERT: C 11 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7566 (pmm-80) REVERT: C 73 ASN cc_start: 0.8553 (t0) cc_final: 0.8187 (t160) REVERT: C 91 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: G 73 ASN cc_start: 0.8468 (t0) cc_final: 0.8185 (t0) REVERT: G 91 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.3583 (tp30) outliers start: 14 outliers final: 9 residues processed: 169 average time/residue: 0.9627 time to fit residues: 170.9287 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085299 restraints weight = 18302.972| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.97 r_work: 0.3102 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12645 Z= 0.139 Angle : 0.647 7.753 18321 Z= 0.376 Chirality : 0.048 0.246 2083 Planarity : 0.004 0.034 1316 Dihedral : 31.126 129.692 4003 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.60 % Allowed : 20.13 % Favored : 77.27 % 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: 3.16 (0.30), residues: 730 helix: 2.88 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.021 0.002 TYR D 83 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.14 (12645) covalent geometry : angle 0.64721 / 0.38 (18321) hydrogen bonds : bond 0.05501 / 3.76 ( 781) hydrogen bonds : angle 2.83324 / 2.13 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4485.29 seconds wall clock time: 76 minutes 54.38 seconds (4614.38 seconds total)