Starting phenix.real_space_refine on Sat Aug 23 09:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jld_36393/08_2025/8jld_36393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jld_36393/08_2025/8jld_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_36393/08_2025/8jld_36393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2025/8jld_36393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2025/8jld_36393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2025/8jld_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): 0.01s 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: 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: 3.00, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 266.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.82 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: 2.21 Time building geometry restraints manager: 1.22 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=" N LYS H 46 " pdb=" CA LYS H 46 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.33e-02 5.65e+03 4.67e+00 bond pdb=" N ARG A 129 " pdb=" CA ARG A 129 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 3.90e+00 bond pdb=" N GLU G 64 " pdb=" CA GLU G 64 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.82e+00 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 17367 1.54 - 3.09: 890 3.09 - 4.63: 49 4.63 - 6.17: 9 6.17 - 7.72: 6 Bond angle restraints: 18321 Sorted by residual: angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.34 118.20 -6.86 1.82e+00 3.02e-01 1.42e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.34 117.68 -6.34 1.82e+00 3.02e-01 1.21e+01 angle pdb=" CG ARG G 35 " pdb=" CD ARG G 35 " pdb=" NE ARG G 35 " ideal model delta sigma weight residual 112.00 119.39 -7.39 2.20e+00 2.07e-01 1.13e+01 angle pdb=" CA MET D 59 " pdb=" CB MET D 59 " pdb=" CG MET D 59 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.82e+00 angle pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" O ARG A 129 " ideal model delta sigma weight residual 120.90 117.85 3.05 1.07e+00 8.73e-01 8.15e+00 ... (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: 1329 0.033 - 0.067: 499 0.067 - 0.100: 190 0.100 - 0.133: 54 0.133 - 0.166: 11 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=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.37e-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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.690 Find NCS groups from input model: 0.090 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.004 0.040 12645 Z= 0.190 Angle : 0.706 7.717 18321 Z= 0.442 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00389 (12645) covalent geometry : angle 0.70559 (18321) hydrogen bonds : bond 0.07192 ( 781) hydrogen bonds : angle 3.35582 ( 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 : 0.286 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: 0.9523 time to fit residues: 162.3372 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 : 0.233 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.7980 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: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 95 GLN F 93 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091398 restraints weight = 18334.824| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.98 r_work: 0.3202 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12645 Z= 0.159 Angle : 0.546 5.159 18321 Z= 0.340 Chirality : 0.033 0.120 2083 Planarity : 0.004 0.033 1316 Dihedral : 30.951 101.440 4005 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.79 % Allowed : 18.67 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.57 (0.31), residues: 730 helix: 3.13 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.05 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.006 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00339 (12645) covalent geometry : angle 0.54642 (18321) hydrogen bonds : bond 0.04370 ( 781) hydrogen bonds : angle 2.74496 ( 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 186 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.191 Fit side-chains REVERT: A 40 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8323 (ttm-80) REVERT: A 58 THR cc_start: 0.8739 (p) cc_final: 0.8521 (t) REVERT: A 129 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7779 (tpt90) REVERT: B 93 GLN cc_start: 0.8323 (mt0) cc_final: 0.7945 (mp10) REVERT: C 11 ARG cc_start: 0.8094 (pmm-80) cc_final: 0.7759 (mtm-85) REVERT: C 13 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8566 (mmmt) REVERT: C 73 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8041 (t160) REVERT: C 77 ARG cc_start: 0.9097 (mtm-85) cc_final: 0.8866 (mtt90) REVERT: D 84 ASN cc_start: 0.8864 (m110) cc_final: 0.8654 (m110) REVERT: E 63 ARG cc_start: 0.8383 (mmp80) cc_final: 0.8124 (mmp80) REVERT: E 129 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7872 (ttp80) REVERT: F 84 MET cc_start: 0.8728 (mmm) cc_final: 0.8492 (mmp) REVERT: F 88 TYR cc_start: 0.8876 (m-10) cc_final: 0.8661 (m-10) REVERT: G 73 ASN cc_start: 0.8366 (t0) cc_final: 0.8055 (t0) REVERT: G 91 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6425 (mm-30) outliers start: 11 outliers final: 5 residues processed: 178 average time/residue: 0.9159 time to fit residues: 171.1634 Evaluate side-chains 175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 47 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086275 restraints weight = 18448.703| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.98 r_work: 0.3108 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12645 Z= 0.214 Angle : 0.582 6.249 18321 Z= 0.359 Chirality : 0.037 0.136 2083 Planarity : 0.004 0.034 1316 Dihedral : 30.671 96.383 4003 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.76 % Allowed : 18.83 % Favored : 78.41 % 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: 3.36 (0.30), residues: 730 helix: 2.99 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.05 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.009 0.002 TYR D 83 PHE 0.010 0.002 PHE A 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00478 (12645) covalent geometry : angle 0.58196 (18321) hydrogen bonds : bond 0.05295 ( 781) hydrogen bonds : angle 2.84796 ( 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 181 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.8334 (ttm170) REVERT: A 83 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8253 (mtt90) REVERT: B 35 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8319 (mtp85) REVERT: C 73 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8161 (t160) REVERT: C 77 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8840 (mtt90) REVERT: C 91 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.3623 (tp30) REVERT: E 63 ARG cc_start: 0.8453 (mmp80) cc_final: 0.8174 (mmp80) REVERT: E 83 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7817 (mtm180) REVERT: F 68 ASP cc_start: 0.8519 (m-30) cc_final: 0.8301 (m-30) REVERT: F 84 MET cc_start: 0.8682 (mmm) cc_final: 0.8458 (mmp) REVERT: F 93 GLN cc_start: 0.8498 (mt0) cc_final: 0.8254 (mt0) REVERT: G 73 ASN cc_start: 0.8436 (t0) cc_final: 0.8117 (t0) REVERT: G 91 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.3641 (tp30) outliers start: 17 outliers final: 6 residues processed: 170 average time/residue: 0.8728 time to fit residues: 155.5717 Evaluate side-chains 171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 64 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084255 restraints weight = 18415.551| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.97 r_work: 0.3088 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12645 Z= 0.254 Angle : 0.593 5.590 18321 Z= 0.365 Chirality : 0.038 0.131 2083 Planarity : 0.004 0.034 1316 Dihedral : 30.414 96.173 4003 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.22 % Allowed : 17.53 % Favored : 78.25 % 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: 3.17 (0.30), residues: 730 helix: 2.86 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 35 TYR 0.009 0.002 TYR F 88 PHE 0.010 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00576 (12645) covalent geometry : angle 0.59252 (18321) hydrogen bonds : bond 0.05444 ( 781) hydrogen bonds : angle 2.84974 ( 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 186 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8251 (mtt90) REVERT: A 129 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7812 (tpt90) REVERT: B 35 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8326 (mtp85) REVERT: B 93 GLN cc_start: 0.8440 (mt0) cc_final: 0.8137 (mm-40) REVERT: C 11 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7180 (pmm-80) REVERT: C 73 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8180 (t160) REVERT: C 91 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: E 83 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7918 (mtm180) REVERT: G 73 ASN cc_start: 0.8443 (t0) cc_final: 0.8153 (t0) REVERT: G 91 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.3655 (tp30) outliers start: 26 outliers final: 10 residues processed: 170 average time/residue: 0.8670 time to fit residues: 154.4661 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 77 LYS 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 G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 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 = 0.3413 r_free = 0.3413 target = 0.097885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085323 restraints weight = 18325.742| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.97 r_work: 0.3106 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12645 Z= 0.175 Angle : 0.577 6.687 18321 Z= 0.357 Chirality : 0.035 0.124 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.448 95.863 4003 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.08 % Allowed : 18.51 % Favored : 78.41 % 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: 3.30 (0.30), residues: 730 helix: 2.96 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.010 0.001 TYR D 40 PHE 0.010 0.001 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00375 (12645) covalent geometry : angle 0.57744 (18321) hydrogen bonds : bond 0.05078 ( 781) hydrogen bonds : angle 2.80774 ( 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 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.327 Fit side-chains REVERT: A 129 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7817 (tpt90) REVERT: B 35 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8329 (mtp85) REVERT: B 93 GLN cc_start: 0.8380 (mt0) cc_final: 0.8059 (mm-40) REVERT: C 11 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7166 (pmm-80) REVERT: C 73 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8193 (t160) REVERT: G 73 ASN cc_start: 0.8427 (t0) cc_final: 0.8144 (t0) REVERT: G 91 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.3619 (tp30) outliers start: 19 outliers final: 10 residues processed: 169 average time/residue: 0.8825 time to fit residues: 156.6521 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 77 LYS 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: 0.5980 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3419 r_free = 0.3419 target = 0.098491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085883 restraints weight = 18342.221| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.97 r_work: 0.3112 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12645 Z= 0.182 Angle : 0.564 5.307 18321 Z= 0.351 Chirality : 0.035 0.124 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.426 95.713 4003 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.76 % Allowed : 19.48 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.34 (0.30), residues: 730 helix: 3.00 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.012 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00398 (12645) covalent geometry : angle 0.56398 (18321) hydrogen bonds : bond 0.04989 ( 781) hydrogen bonds : angle 2.76609 ( 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 179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.185 Fit side-chains REVERT: A 129 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7822 (tpt90) REVERT: B 35 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8327 (mtp85) REVERT: B 93 GLN cc_start: 0.8369 (mt0) cc_final: 0.8024 (mm-40) REVERT: C 11 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7233 (pmm-80) REVERT: C 73 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8158 (t160) REVERT: C 91 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.3520 (tp30) REVERT: G 73 ASN cc_start: 0.8415 (t0) cc_final: 0.8129 (t0) REVERT: G 91 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.3584 (tp30) outliers start: 17 outliers final: 11 residues processed: 169 average time/residue: 0.8501 time to fit residues: 150.8012 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS 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 G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086427 restraints weight = 18262.974| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 0.97 r_work: 0.3123 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12645 Z= 0.164 Angle : 0.567 10.706 18321 Z= 0.350 Chirality : 0.034 0.124 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.429 95.264 4003 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.76 % Allowed : 19.81 % Favored : 77.44 % 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: 3.36 (0.30), residues: 730 helix: 3.00 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.018 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00350 (12645) covalent geometry : angle 0.56705 (18321) hydrogen bonds : bond 0.04831 ( 781) hydrogen bonds : angle 2.76215 ( 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 179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.263 Fit side-chains REVERT: A 129 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7831 (tpt90) REVERT: B 35 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8329 (mtp85) REVERT: B 93 GLN cc_start: 0.8408 (mt0) cc_final: 0.8095 (mm-40) REVERT: C 73 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8188 (t160) REVERT: C 91 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.3486 (tp30) REVERT: E 53 ARG cc_start: 0.8684 (tmm-80) cc_final: 0.8481 (ttt-90) REVERT: G 73 ASN cc_start: 0.8409 (t0) cc_final: 0.8120 (t0) REVERT: G 91 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.3589 (tp30) outliers start: 17 outliers final: 12 residues processed: 169 average time/residue: 0.8529 time to fit residues: 151.1347 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR 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 115 LYS Chi-restraints excluded: chain F residue 77 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 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 = 0.3391 r_free = 0.3391 target = 0.096526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083977 restraints weight = 18442.308| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 0.98 r_work: 0.3082 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12645 Z= 0.255 Angle : 0.596 6.042 18321 Z= 0.367 Chirality : 0.038 0.137 2083 Planarity : 0.004 0.033 1316 Dihedral : 30.359 95.967 4003 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.73 % Allowed : 19.32 % Favored : 76.95 % 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: 3.13 (0.30), residues: 730 helix: 2.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 53 TYR 0.015 0.002 TYR D 83 PHE 0.009 0.002 PHE A 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00579 (12645) covalent geometry : angle 0.59649 (18321) hydrogen bonds : bond 0.05421 ( 781) hydrogen bonds : angle 2.85767 ( 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 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.277 Fit side-chains REVERT: A 118 THR cc_start: 0.9072 (m) cc_final: 0.8871 (m) REVERT: A 129 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7828 (tpt90) REVERT: B 35 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8354 (mtp85) REVERT: B 93 GLN cc_start: 0.8399 (mt0) cc_final: 0.8103 (mm-40) REVERT: B 95 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8043 (mtp-110) REVERT: C 11 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7199 (pmm-80) REVERT: C 73 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8196 (t160) REVERT: C 91 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.5751 (mp0) REVERT: G 73 ASN cc_start: 0.8452 (t0) cc_final: 0.8171 (t0) REVERT: G 91 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.3661 (tp30) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.9026 time to fit residues: 156.0138 Evaluate side-chains 171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 115 LYS 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 G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL 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: 0.8980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084457 restraints weight = 18201.619| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.96 r_work: 0.3091 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12645 Z= 0.214 Angle : 0.595 9.520 18321 Z= 0.364 Chirality : 0.036 0.128 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.377 96.023 4003 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.57 % Allowed : 19.48 % Favored : 76.95 % 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: 3.16 (0.30), residues: 730 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.018 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00477 (12645) covalent geometry : angle 0.59510 (18321) hydrogen bonds : bond 0.05275 ( 781) hydrogen bonds : angle 2.84288 ( 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 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.297 Fit side-chains REVERT: A 83 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8245 (mtt90) REVERT: A 118 THR cc_start: 0.9075 (m) cc_final: 0.8872 (m) REVERT: A 129 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7827 (tpt90) REVERT: B 35 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8348 (mtp85) REVERT: B 93 GLN cc_start: 0.8442 (mt0) cc_final: 0.8158 (mm-40) REVERT: B 95 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8027 (mtp-110) REVERT: C 11 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7198 (pmm-80) REVERT: C 73 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8190 (t160) REVERT: C 91 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: G 73 ASN cc_start: 0.8450 (t0) cc_final: 0.8166 (t0) REVERT: G 91 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.3641 (tp30) outliers start: 22 outliers final: 14 residues processed: 163 average time/residue: 0.9125 time to fit residues: 156.1405 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 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 B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 115 LYS 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 G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL 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 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084313 restraints weight = 18430.268| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.98 r_work: 0.3088 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12645 Z= 0.234 Angle : 0.596 10.515 18321 Z= 0.364 Chirality : 0.037 0.133 2083 Planarity : 0.004 0.033 1316 Dihedral : 30.365 95.948 4003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 19.81 % Favored : 76.79 % 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: 3.12 (0.30), residues: 730 helix: 2.80 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.08 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.020 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00530 (12645) covalent geometry : angle 0.59563 (18321) hydrogen bonds : bond 0.05312 ( 781) hydrogen bonds : angle 2.83558 ( 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 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.325 Fit side-chains REVERT: A 83 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8248 (mtt90) REVERT: A 118 THR cc_start: 0.9078 (m) cc_final: 0.8875 (m) REVERT: A 129 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7822 (tpt90) REVERT: B 35 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8350 (mtp85) REVERT: B 93 GLN cc_start: 0.8443 (mt0) cc_final: 0.8156 (mm-40) REVERT: B 95 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8080 (mtp-110) REVERT: C 11 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7203 (pmm-80) REVERT: C 73 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8194 (t160) REVERT: C 91 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: G 73 ASN cc_start: 0.8452 (t0) cc_final: 0.8167 (t0) REVERT: G 91 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.3657 (tp30) outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.9226 time to fit residues: 158.4116 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 115 LYS 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 G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL 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: 5.9990 chunk 15 optimal weight: 0.0270 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084597 restraints weight = 18324.870| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.97 r_work: 0.3093 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12645 Z= 0.207 Angle : 0.586 6.373 18321 Z= 0.360 Chirality : 0.036 0.130 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.371 96.037 4003 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 19.81 % Favored : 76.79 % 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: 3.16 (0.30), residues: 730 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.019 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 covalent geometry : bond 0.00459 (12645) covalent geometry : angle 0.58551 (18321) hydrogen bonds : bond 0.05230 ( 781) hydrogen bonds : angle 2.82889 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.21 seconds wall clock time: 74 minutes 1.58 seconds (4441.58 seconds total)