Starting phenix.real_space_refine on Tue Aug 4 15:18:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2026/7yr6_34047.cif" } resolution = 4.8 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= 0.004 sd= 0.039 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 118 5.49 5 S 8 5.16 5 C 2197 2.51 5 N 797 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNAv2': 118} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 7, 'rna3p_pur': 52, 'rna3p_pyr': 39} Link IDs: {'rna2p': 26, 'rna3p': 91} Time building chain proxies: 1.20, per 1000 atoms: 0.28 Number of scatterers: 4248 At special positions: 0 Unit cell: (84.15, 91.8, 101.15, 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 8 16.00 P 118 15.00 O 1128 8.00 N 797 7.00 C 2197 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: 0.31 Conformation dependent library (CDL) restraints added in 44.5 milliseconds 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 398 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 3 sheets defined 14.1% alpha, 14.1% beta 30 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'B' and resid 45 through 49 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.787A pdb=" N GLY D 33 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 26 removed outlier: 5.104A pdb=" N VAL C 22 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 33 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 30 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 6 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.744A pdb=" N THR B 21 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 33 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 672 1.33 - 1.45: 1678 1.45 - 1.57: 1962 1.57 - 1.69: 235 1.69 - 1.80: 16 Bond restraints: 4563 Sorted by residual: bond pdb=" O3' C A 15 " pdb=" P G A 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" O3' G A 57 " pdb=" P A A 58 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" O3' C A 61 " pdb=" P C A 62 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.37e+01 bond pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" O3' A A 63 " pdb=" P U A 64 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.20e-02 6.94e+03 8.25e+00 ... (remaining 4558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 6008 1.74 - 3.48: 580 3.48 - 5.23: 145 5.23 - 6.97: 18 6.97 - 8.71: 5 Bond angle restraints: 6756 Sorted by residual: angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" C3' C A 61 " pdb=" O3' C A 61 " pdb=" P C A 62 " ideal model delta sigma weight residual 119.70 125.24 -5.54 1.20e+00 6.94e-01 2.13e+01 angle pdb=" C ILE E 47 " pdb=" N TYR E 48 " pdb=" CA TYR E 48 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" N LEU E 23 " pdb=" CA LEU E 23 " pdb=" C LEU E 23 " ideal model delta sigma weight residual 110.88 116.23 -5.35 1.28e+00 6.10e-01 1.75e+01 angle pdb=" C GLU E 45 " pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 2100 35.86 - 71.71: 345 71.71 - 107.57: 25 107.57 - 143.42: 0 143.42 - 179.28: 1 Dihedral angle restraints: 2471 sinusoidal: 1853 harmonic: 618 Sorted by residual: dihedral pdb=" C4' U A 59 " pdb=" C3' U A 59 " pdb=" C2' U A 59 " pdb=" C1' U A 59 " ideal model delta sinusoidal sigma weight residual 36.34 -43.21 79.55 1 3.10e+00 1.04e-01 8.18e+02 dihedral pdb=" C4' G A 81 " pdb=" C3' G A 81 " pdb=" C2' G A 81 " pdb=" C1' G A 81 " ideal model delta sinusoidal sigma weight residual 36.34 -42.71 79.05 1 3.10e+00 1.04e-01 8.09e+02 dihedral pdb=" C4' A A 63 " pdb=" C3' A A 63 " pdb=" C2' A A 63 " pdb=" C1' A A 63 " ideal model delta sinusoidal sigma weight residual 36.35 -41.31 77.66 1 3.10e+00 1.04e-01 7.85e+02 ... (remaining 2468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 660 0.109 - 0.217: 61 0.217 - 0.326: 152 0.326 - 0.434: 1 0.434 - 0.543: 2 Chirality restraints: 876 Sorted by residual: chirality pdb=" P G A 57 " pdb=" OP1 G A 57 " pdb=" OP2 G A 57 " pdb=" O5' G A 57 " both_signs ideal model delta sigma weight residual True 2.17 -2.72 -0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" P G A 81 " pdb=" OP1 G A 81 " pdb=" OP2 G A 81 " pdb=" O5' G A 81 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" CB ILE C 32 " pdb=" CA ILE C 32 " pdb=" CG1 ILE C 32 " pdb=" CG2 ILE C 32 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 873 not shown) Planarity restraints: 413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 35 " -0.022 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" N9 G A 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A 35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 91 " 0.021 2.00e-02 2.50e+03 1.08e-02 2.63e+00 pdb=" N1 U A 91 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U A 91 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 91 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 91 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U A 91 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 91 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 48 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C TYR E 48 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR E 48 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN E 49 " -0.009 2.00e-02 2.50e+03 ... (remaining 410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1060 2.81 - 3.33: 3678 3.33 - 3.86: 8638 3.86 - 4.38: 9229 4.38 - 4.90: 12472 Nonbonded interactions: 35077 Sorted by model distance: nonbonded pdb=" O2' G A 50 " pdb=" O4' G A 51 " model vdw 2.291 3.040 nonbonded pdb=" O2' A A 41 " pdb=" O5' G A 43 " model vdw 2.326 3.040 nonbonded pdb=" O GLU B 10 " pdb=" OG1 THR B 21 " model vdw 2.342 3.040 nonbonded pdb=" O VAL E 40 " pdb=" N1 G A 10 " model vdw 2.370 3.120 nonbonded pdb=" O VAL B 42 " pdb=" N2 G A 39 " model vdw 2.397 3.120 ... (remaining 35072 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 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.005 0.059 4563 Z= 0.283 Angle : 1.163 8.709 6756 Z= 0.550 Chirality : 0.122 0.543 876 Planarity : 0.004 0.028 413 Dihedral : 25.339 179.280 2073 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 3.30 % Allowed : 12.09 % Favored : 84.62 % 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: -5.39 (0.42), residues: 212 helix: -3.34 (0.76), residues: 24 sheet: -3.13 (0.95), residues: 29 loop : -4.07 (0.34), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.008 0.001 TYR B 48 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.28 ( 4563) covalent geometry : angle 1.16253 / 0.55 ( 6756) hydrogen bonds : bond 0.13349 / 9.96 ( 110) hydrogen bonds : angle 5.47836 / 3.83 ( 232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9402 (tmm) cc_final: 0.9171 (tmm) REVERT: E 46 GLU cc_start: 0.9307 (tp30) cc_final: 0.8712 (tp30) REVERT: E 47 ILE cc_start: 0.8852 (mt) cc_final: 0.8353 (mp) REVERT: C 43 HIS cc_start: 0.9032 (m-70) cc_final: 0.8789 (m90) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.0952 time to fit residues: 9.2151 Evaluate side-chains 59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.071233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.056234 restraints weight = 38873.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057875 restraints weight = 22219.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059035 restraints weight = 14854.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059810 restraints weight = 11110.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060373 restraints weight = 8969.130| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4563 Z= 0.274 Angle : 1.474 14.100 6756 Z= 0.609 Chirality : 0.111 0.730 876 Planarity : 0.005 0.030 413 Dihedral : 22.075 179.627 1653 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Rotamer: Outliers : 0.55 % Allowed : 9.89 % Favored : 89.56 % 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: -5.21 (0.47), residues: 212 helix: -2.55 (0.90), residues: 28 sheet: -2.84 (0.99), residues: 24 loop : -4.10 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 31 TYR 0.008 0.002 TYR E 48 HIS 0.006 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.27 ( 4563) covalent geometry : angle 1.47361 / 0.61 ( 6756) hydrogen bonds : bond 0.07593 / 5.19 ( 110) hydrogen bonds : angle 4.73059 / 3.23 ( 232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9530 (tmm) cc_final: 0.9159 (tmm) REVERT: E 47 ILE cc_start: 0.8849 (mt) cc_final: 0.8509 (mp) REVERT: C 2 LEU cc_start: 0.8232 (mm) cc_final: 0.7903 (mm) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.1017 time to fit residues: 7.0396 Evaluate side-chains 47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056910 restraints weight = 37087.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058651 restraints weight = 21479.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059851 restraints weight = 14410.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060677 restraints weight = 10739.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061304 restraints weight = 8597.490| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4563 Z= 0.186 Angle : 1.067 10.112 6756 Z= 0.451 Chirality : 0.078 0.471 876 Planarity : 0.004 0.030 413 Dihedral : 22.204 173.840 1653 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.92 % Favored : 82.08 % Rotamer: Outliers : 0.55 % Allowed : 9.89 % Favored : 89.56 % 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: -4.88 (0.49), residues: 212 helix: -1.94 (0.97), residues: 28 sheet: -2.38 (1.13), residues: 22 loop : -3.99 (0.40), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 50 TYR 0.013 0.002 TYR E 48 HIS 0.004 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 ( 4563) covalent geometry : angle 1.06665 / 0.45 ( 6756) hydrogen bonds : bond 0.05046 / 3.36 ( 110) hydrogen bonds : angle 4.24446 / 2.97 ( 232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8949 (ttp) cc_final: 0.8671 (tmm) REVERT: E 7 ARG cc_start: 0.9407 (tpp-160) cc_final: 0.9194 (tpp80) REVERT: E 13 MET cc_start: 0.9548 (tmm) cc_final: 0.9188 (tmm) REVERT: C 2 LEU cc_start: 0.8595 (mm) cc_final: 0.8374 (mm) REVERT: C 31 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8884 (ttt180) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.1267 time to fit residues: 9.0135 Evaluate side-chains 52 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045904 restraints weight = 38617.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047464 restraints weight = 21905.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048557 restraints weight = 14716.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049250 restraints weight = 11025.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049795 restraints weight = 8997.660| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 4563 Z= 0.463 Angle : 1.523 12.024 6756 Z= 0.635 Chirality : 0.095 0.472 876 Planarity : 0.009 0.081 413 Dihedral : 22.843 179.512 1653 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 52.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.47 % Favored : 74.53 % Rotamer: Outliers : 1.10 % Allowed : 16.48 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.32 (0.49), residues: 212 helix: -2.59 (0.83), residues: 28 sheet: -3.34 (1.31), residues: 12 loop : -4.13 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 44 TYR 0.029 0.003 TYR E 48 HIS 0.012 0.005 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.46 ( 4563) covalent geometry : angle 1.52293 / 0.64 ( 6756) hydrogen bonds : bond 0.15159 / 10.73 ( 110) hydrogen bonds : angle 5.04274 / 3.31 ( 232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9131 (ttp) cc_final: 0.8890 (tmm) REVERT: E 7 ARG cc_start: 0.9472 (tpp-160) cc_final: 0.9197 (tpp80) REVERT: C 2 LEU cc_start: 0.8166 (mm) cc_final: 0.7948 (mm) REVERT: B 23 LEU cc_start: 0.9570 (mm) cc_final: 0.9305 (mm) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.0847 time to fit residues: 5.2994 Evaluate side-chains 48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.070060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054975 restraints weight = 38392.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056772 restraints weight = 22049.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057992 restraints weight = 14705.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058757 restraints weight = 10949.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059430 restraints weight = 8873.331| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4563 Z= 0.181 Angle : 1.073 10.762 6756 Z= 0.456 Chirality : 0.076 0.488 876 Planarity : 0.004 0.022 413 Dihedral : 22.423 175.391 1653 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.11 (0.49), residues: 212 helix: -3.16 (0.69), residues: 30 sheet: -3.37 (0.99), residues: 22 loop : -3.77 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 44 TYR 0.026 0.003 TYR E 48 HIS 0.009 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 4563) covalent geometry : angle 1.07346 / 0.46 ( 6756) hydrogen bonds : bond 0.05468 / 3.58 ( 110) hydrogen bonds : angle 4.67197 / 3.13 ( 232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8913 (ttp) cc_final: 0.8453 (ppp) REVERT: E 7 ARG cc_start: 0.9288 (tpp-160) cc_final: 0.9011 (tpp80) REVERT: D 13 MET cc_start: 0.5829 (ppp) cc_final: 0.5450 (ppp) REVERT: D 48 TYR cc_start: 0.9172 (t80) cc_final: 0.8899 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0697 time to fit residues: 4.9367 Evaluate side-chains 48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 8 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054558 restraints weight = 39138.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056362 restraints weight = 22326.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057628 restraints weight = 14814.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058435 restraints weight = 10959.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059065 restraints weight = 8802.288| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4563 Z= 0.188 Angle : 1.039 10.353 6756 Z= 0.445 Chirality : 0.073 0.485 876 Planarity : 0.004 0.044 413 Dihedral : 22.081 175.870 1653 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % Rotamer: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -4.98 (0.51), residues: 212 helix: -3.81 (0.56), residues: 28 sheet: -2.60 (1.18), residues: 22 loop : -3.64 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.020 0.003 TYR E 48 HIS 0.004 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 4563) covalent geometry : angle 1.03854 / 0.44 ( 6756) hydrogen bonds : bond 0.06065 / 4.04 ( 110) hydrogen bonds : angle 4.57851 / 3.21 ( 232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8857 (ttp) cc_final: 0.8358 (ppp) REVERT: E 7 ARG cc_start: 0.9325 (tpp-160) cc_final: 0.9012 (tpp80) REVERT: E 44 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6906 (mtt180) REVERT: D 13 MET cc_start: 0.5410 (ppp) cc_final: 0.5087 (ppp) REVERT: D 48 TYR cc_start: 0.9367 (t80) cc_final: 0.9112 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0983 time to fit residues: 7.0011 Evaluate side-chains 50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052029 restraints weight = 39640.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053683 restraints weight = 23125.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054878 restraints weight = 15655.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055586 restraints weight = 11696.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056194 restraints weight = 9567.807| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4563 Z= 0.257 Angle : 1.121 10.320 6756 Z= 0.477 Chirality : 0.076 0.465 876 Planarity : 0.006 0.062 413 Dihedral : 22.286 177.680 1653 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.93 (0.52), residues: 212 helix: -3.59 (0.62), residues: 28 sheet: -2.70 (1.14), residues: 22 loop : -3.62 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.011 0.002 TYR B 48 HIS 0.007 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 ( 4563) covalent geometry : angle 1.12056 / 0.48 ( 6756) hydrogen bonds : bond 0.08318 / 5.72 ( 110) hydrogen bonds : angle 4.54953 / 3.14 ( 232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8802 (ttp) cc_final: 0.8589 (ppp) REVERT: E 7 ARG cc_start: 0.9344 (tpp-160) cc_final: 0.9029 (tpp80) REVERT: E 44 ARG cc_start: 0.7521 (ptp-170) cc_final: 0.7317 (ptp-170) REVERT: D 1 MET cc_start: 0.6174 (tpt) cc_final: 0.5842 (tpt) REVERT: D 48 TYR cc_start: 0.9325 (t80) cc_final: 0.9053 (t80) REVERT: D 50 ARG cc_start: 0.9500 (ptt180) cc_final: 0.9264 (ptt180) REVERT: C 31 ARG cc_start: 0.9093 (mtt180) cc_final: 0.8816 (ttt180) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0880 time to fit residues: 5.9208 Evaluate side-chains 48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049873 restraints weight = 40208.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.051496 restraints weight = 23129.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052618 restraints weight = 15612.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053312 restraints weight = 11729.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053910 restraints weight = 9632.104| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4563 Z= 0.308 Angle : 1.227 9.931 6756 Z= 0.524 Chirality : 0.081 0.451 876 Planarity : 0.007 0.055 413 Dihedral : 22.573 179.445 1653 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 37.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.14 (0.48), residues: 212 helix: -3.46 (0.66), residues: 28 sheet: -3.18 (1.31), residues: 12 loop : -3.81 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG C 6 TYR 0.010 0.003 TYR C 48 HIS 0.007 0.004 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 ( 4563) covalent geometry : angle 1.22727 / 0.52 ( 6756) hydrogen bonds : bond 0.10078 / 6.94 ( 110) hydrogen bonds : angle 4.97466 / 3.41 ( 232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8912 (ttp) cc_final: 0.8669 (tmm) REVERT: E 7 ARG cc_start: 0.9387 (tpp-160) cc_final: 0.9129 (tpp80) REVERT: E 47 ILE cc_start: 0.8422 (mp) cc_final: 0.7901 (mp) REVERT: D 1 MET cc_start: 0.6211 (tpt) cc_final: 0.5986 (tpt) REVERT: D 13 MET cc_start: 0.6081 (ppp) cc_final: 0.5867 (ppp) REVERT: D 48 TYR cc_start: 0.9340 (t80) cc_final: 0.9118 (t80) REVERT: C 31 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8922 (ttt180) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0853 time to fit residues: 5.4181 Evaluate side-chains 45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.0000 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053774 restraints weight = 39197.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055566 restraints weight = 22326.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.056787 restraints weight = 14893.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057557 restraints weight = 11110.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058163 restraints weight = 9020.251| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4563 Z= 0.186 Angle : 1.057 10.340 6756 Z= 0.454 Chirality : 0.074 0.488 876 Planarity : 0.005 0.048 413 Dihedral : 22.058 177.824 1653 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -4.98 (0.50), residues: 212 helix: -3.89 (0.57), residues: 28 sheet: -3.24 (1.01), residues: 22 loop : -3.52 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 50 TYR 0.022 0.003 TYR B 48 HIS 0.007 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 4563) covalent geometry : angle 1.05672 / 0.45 ( 6756) hydrogen bonds : bond 0.05632 / 3.75 ( 110) hydrogen bonds : angle 4.59231 / 3.18 ( 232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8866 (ttp) cc_final: 0.8554 (ppp) REVERT: D 13 MET cc_start: 0.5821 (ppp) cc_final: 0.5575 (ppp) REVERT: C 31 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8676 (ttt180) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1111 time to fit residues: 7.4152 Evaluate side-chains 46 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051825 restraints weight = 38994.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053540 restraints weight = 22118.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054726 restraints weight = 14776.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055531 restraints weight = 11042.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055994 restraints weight = 8914.608| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4563 Z= 0.232 Angle : 1.096 9.890 6756 Z= 0.469 Chirality : 0.076 0.462 876 Planarity : 0.005 0.048 413 Dihedral : 22.005 177.339 1653 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -4.86 (0.50), residues: 212 helix: -3.86 (0.61), residues: 28 sheet: -3.01 (1.35), residues: 12 loop : -3.48 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 50 TYR 0.012 0.002 TYR E 48 HIS 0.007 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 ( 4563) covalent geometry : angle 1.09605 / 0.47 ( 6756) hydrogen bonds : bond 0.07385 / 5.04 ( 110) hydrogen bonds : angle 4.65026 / 3.22 ( 232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8848 (ttp) cc_final: 0.8523 (ppp) REVERT: D 48 TYR cc_start: 0.9300 (t80) cc_final: 0.9088 (t80) REVERT: C 31 ARG cc_start: 0.9062 (mtt180) cc_final: 0.8713 (ttt180) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0940 time to fit residues: 6.2105 Evaluate side-chains 49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052489 restraints weight = 38685.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054220 restraints weight = 22249.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055432 restraints weight = 14976.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056197 restraints weight = 11239.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056807 restraints weight = 9164.035| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4563 Z= 0.209 Angle : 1.071 10.010 6756 Z= 0.459 Chirality : 0.074 0.469 876 Planarity : 0.005 0.046 413 Dihedral : 21.892 176.018 1653 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % Rotamer: Outliers : 0.55 % Allowed : 0.55 % Favored : 98.90 % 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: -4.98 (0.49), residues: 212 helix: -3.86 (0.64), residues: 28 sheet: -3.50 (0.89), residues: 22 loop : -3.48 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.021 0.003 TYR B 48 HIS 0.005 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 ( 4563) covalent geometry : angle 1.07097 / 0.46 ( 6756) hydrogen bonds : bond 0.06776 / 4.58 ( 110) hydrogen bonds : angle 4.53033 / 3.15 ( 232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 756.66 seconds wall clock time: 13 minutes 43.93 seconds (823.93 seconds total)