Starting phenix.real_space_refine on Wed Aug 5 05:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.map" model { file = "/net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv5_53386/08_2026/9qv5_53386.cif" } resolution = 3.5 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= 0.000 sd= 0.002 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 240 5.49 5 S 12 5.16 5 C 4551 2.51 5 N 1659 2.21 5 O 2166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 8628 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "D" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "E" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "F" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'TRANS': 67} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 273 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 63} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "H" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 273 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 63} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "X" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2446 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Chain: "Y" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2474 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Time building chain proxies: 1.49, per 1000 atoms: 0.17 Number of scatterers: 8628 At special positions: 0 Unit cell: (86.505, 113.88, 112.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 240 15.00 O 2166 8.00 N 1659 7.00 C 4551 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: 0.53 Conformation dependent library (CDL) restraints added in 211.4 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 77.2% alpha, 2.9% beta 118 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 23 through 52 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 23 through 52 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 23 through 53 Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 23 through 52 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 23 through 52 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 23 through 52 Processing helix chain 'F' and resid 58 through 67 Processing helix chain 'G' and resid 6 through 17 Processing helix chain 'G' and resid 23 through 53 removed outlier: 4.135A pdb=" N TYR G 44 " --> pdb=" O ASN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.581A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 23 through 52 removed outlier: 3.553A pdb=" N ASP H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR H 44 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 68 removed outlier: 3.528A pdb=" N ILE H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 7.030A pdb=" N ARG A 21 " --> pdb=" O VAL B 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.068A pdb=" N ARG C 21 " --> pdb=" O VAL D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22 removed outlier: 7.104A pdb=" N ARG E 21 " --> pdb=" O VAL F 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 21 through 22 removed outlier: 7.261A pdb=" N ARG G 21 " --> pdb=" O VAL H 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 323 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 295 hydrogen bonds 590 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1104 1.32 - 1.44: 3277 1.44 - 1.56: 4365 1.56 - 1.69: 478 1.69 - 1.81: 24 Bond restraints: 9248 Sorted by residual: bond pdb=" CA SER D 23 " pdb=" CB SER D 23 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.53e-02 4.27e+03 2.09e+01 bond pdb=" CA SER F 23 " pdb=" CB SER F 23 " ideal model delta sigma weight residual 1.529 1.470 0.060 1.58e-02 4.01e+03 1.42e+01 bond pdb=" C ASP D 61 " pdb=" O ASP D 61 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.15e-02 7.56e+03 1.40e+01 bond pdb=" CA SER E 23 " pdb=" CB SER E 23 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.66e-02 3.63e+03 1.35e+01 bond pdb=" CA SER A 23 " pdb=" CB SER A 23 " ideal model delta sigma weight residual 1.528 1.469 0.060 1.66e-02 3.63e+03 1.30e+01 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 9841 1.81 - 3.62: 2974 3.62 - 5.43: 575 5.43 - 7.23: 54 7.23 - 9.04: 6 Bond angle restraints: 13450 Sorted by residual: angle pdb=" N VAL H 10 " pdb=" CA VAL H 10 " pdb=" C VAL H 10 " ideal model delta sigma weight residual 111.00 101.96 9.04 1.09e+00 8.42e-01 6.88e+01 angle pdb=" O5' DG Y 50 " pdb=" C5' DG Y 50 " pdb=" C4' DG Y 50 " ideal model delta sigma weight residual 109.40 115.64 -6.24 8.00e-01 1.56e+00 6.09e+01 angle pdb=" O5' DC X 61 " pdb=" C5' DC X 61 " pdb=" C4' DC X 61 " ideal model delta sigma weight residual 109.40 115.42 -6.02 8.00e-01 1.56e+00 5.66e+01 angle pdb=" N VAL H 27 " pdb=" CA VAL H 27 " pdb=" C VAL H 27 " ideal model delta sigma weight residual 110.42 104.00 6.42 9.60e-01 1.09e+00 4.47e+01 angle pdb=" O5' DT X 76 " pdb=" C5' DT X 76 " pdb=" C4' DT X 76 " ideal model delta sigma weight residual 109.40 114.60 -5.20 8.00e-01 1.56e+00 4.22e+01 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 3669 35.48 - 70.96: 1025 70.96 - 106.44: 21 106.44 - 141.92: 0 141.92 - 177.40: 3 Dihedral angle restraints: 4718 sinusoidal: 3408 harmonic: 1310 Sorted by residual: dihedral pdb=" CD ARG F 54 " pdb=" NE ARG F 54 " pdb=" CZ ARG F 54 " pdb=" NH1 ARG F 54 " ideal model delta sinusoidal sigma weight residual 0.00 86.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CD ARG C 9 " pdb=" NE ARG C 9 " pdb=" CZ ARG C 9 " pdb=" NH1 ARG C 9 " ideal model delta sinusoidal sigma weight residual 0.00 41.72 -41.72 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CD ARG F 9 " pdb=" NE ARG F 9 " pdb=" CZ ARG F 9 " pdb=" NH1 ARG F 9 " ideal model delta sinusoidal sigma weight residual 0.00 38.05 -38.05 1 1.00e+01 1.00e-02 2.04e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.135: 1126 0.135 - 0.270: 149 0.270 - 0.405: 155 0.405 - 0.540: 2 0.540 - 0.674: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" P DT Y 1 " pdb=" OP1 DT Y 1 " pdb=" OP2 DT Y 1 " pdb=" O5' DT Y 1 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" P DG X 1 " pdb=" OP1 DG X 1 " pdb=" OP2 DG X 1 " pdb=" O5' DG X 1 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" P DC X 96 " pdb=" OP1 DC X 96 " pdb=" OP2 DC X 96 " pdb=" O5' DC X 96 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1431 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 54 " 1.139 9.50e-02 1.11e+02 5.11e-01 1.57e+02 pdb=" NE ARG F 54 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG F 54 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG F 54 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG F 54 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 9 " 0.717 9.50e-02 1.11e+02 3.21e-01 6.30e+01 pdb=" NE ARG C 9 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG C 9 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 9 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 9 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 37 " 0.087 2.00e-02 2.50e+03 4.73e-02 5.59e+01 pdb=" CG TRP C 37 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 37 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 37 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP C 37 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP C 37 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP C 37 " -0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 37 " 0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 37 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 37 " 0.071 2.00e-02 2.50e+03 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 725 2.74 - 3.28: 7403 3.28 - 3.82: 14782 3.82 - 4.36: 20397 4.36 - 4.90: 28093 Nonbonded interactions: 71400 Sorted by model distance: nonbonded pdb=" N2 DG X 58 " pdb=" N2 DG Y 64 " model vdw 2.202 3.200 nonbonded pdb=" N6 DA X 93 " pdb=" O6 DG Y 27 " model vdw 2.207 3.120 nonbonded pdb=" O6 DG X 42 " pdb=" O6 DG Y 78 " model vdw 2.234 3.040 nonbonded pdb=" N4 DC X 68 " pdb=" O6 DG Y 52 " model vdw 2.246 3.120 nonbonded pdb=" C2 DG X 58 " pdb=" N2 DG Y 64 " model vdw 2.252 3.340 ... (remaining 71395 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' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = (chain 'B' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = (chain 'C' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = (chain 'D' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = (chain 'E' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = (chain 'F' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ ) or (resid 68 and (name N or name CA or name C or name O or name OXT)))) selection = chain 'G' 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=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: 26.240 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: 0.680 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.012 0.070 9248 Z= 0.862 Angle : 1.698 9.044 13450 Z= 1.256 Chirality : 0.139 0.674 1434 Planarity : 0.040 0.511 934 Dihedral : 29.238 177.397 3950 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.64 % Allowed : 4.17 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.32), residues: 528 helix: -0.69 (0.23), residues: 424 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG F 9 TYR 0.016 0.005 TYR E 44 PHE 0.035 0.014 PHE B 5 TRP 0.087 0.034 TRP C 37 HIS 0.007 0.003 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01210 / 0.86 ( 9248) covalent geometry : angle 1.69807 / 1.26 (13450) hydrogen bonds : bond 0.20001 / 13.33 ( 618) hydrogen bonds : angle 7.48568 / 5.34 ( 1559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8491 (tpt) cc_final: 0.8267 (tpp) REVERT: B 41 ILE cc_start: 0.8661 (mt) cc_final: 0.8392 (tt) REVERT: C 1 MET cc_start: 0.3939 (ttt) cc_final: 0.3530 (ttt) REVERT: F 52 SER cc_start: 0.8765 (t) cc_final: 0.8551 (m) REVERT: F 56 THR cc_start: 0.9195 (m) cc_final: 0.8813 (p) REVERT: F 64 LEU cc_start: 0.9345 (tp) cc_final: 0.9003 (mp) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1072 time to fit residues: 12.2803 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN C 4 ASN D 4 ASN E 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.164811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111217 restraints weight = 14493.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115137 restraints weight = 8438.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.116056 restraints weight = 5700.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116420 restraints weight = 5142.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116498 restraints weight = 4697.838| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 9248 Z= 0.416 Angle : 1.138 10.758 13450 Z= 0.604 Chirality : 0.072 0.303 1434 Planarity : 0.007 0.065 934 Dihedral : 32.644 179.071 3170 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.21 % Allowed : 10.26 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.34), residues: 528 helix: 0.73 (0.23), residues: 432 sheet: None (None), residues: 0 loop : -1.10 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 15 TYR 0.012 0.002 TYR A 44 PHE 0.020 0.004 PHE D 5 TRP 0.028 0.005 TRP C 37 HIS 0.007 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.42 ( 9248) covalent geometry : angle 1.13803 / 0.60 (13450) hydrogen bonds : bond 0.08684 / 5.68 ( 618) hydrogen bonds : angle 3.89876 / 2.84 ( 1559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8149 (mtmm) REVERT: D 30 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8507 (tpt) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.1101 time to fit residues: 12.5476 Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 50.0000 chunk 61 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 ASN D 67 GLN E 4 ASN F 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.169821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115486 restraints weight = 14283.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120090 restraints weight = 7156.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121668 restraints weight = 4749.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122909 restraints weight = 3720.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123064 restraints weight = 3637.451| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9248 Z= 0.230 Angle : 0.775 8.360 13450 Z= 0.449 Chirality : 0.054 0.312 1434 Planarity : 0.004 0.029 934 Dihedral : 32.662 177.719 3170 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.49 % Allowed : 13.46 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.35), residues: 528 helix: 1.91 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.91 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.014 0.002 TYR F 44 PHE 0.017 0.003 PHE D 5 TRP 0.019 0.004 TRP F 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 ( 9248) covalent geometry : angle 0.77550 / 0.45 (13450) hydrogen bonds : bond 0.05663 / 3.79 ( 618) hydrogen bonds : angle 3.12055 / 2.26 ( 1559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8785 (ttmt) REVERT: A 55 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8185 (mtmm) REVERT: B 23 SER cc_start: 0.8890 (p) cc_final: 0.8574 (t) outliers start: 14 outliers final: 14 residues processed: 80 average time/residue: 0.1029 time to fit residues: 10.7788 Evaluate side-chains 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 GLN E 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115915 restraints weight = 14333.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120084 restraints weight = 7343.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121371 restraints weight = 5129.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122456 restraints weight = 4008.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.122647 restraints weight = 3877.736| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9248 Z= 0.161 Angle : 0.717 8.031 13450 Z= 0.415 Chirality : 0.051 0.320 1434 Planarity : 0.003 0.028 934 Dihedral : 32.450 176.086 3170 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 15.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.36), residues: 528 helix: 2.80 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.94 (0.54), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 15 TYR 0.011 0.002 TYR A 44 PHE 0.010 0.002 PHE D 5 TRP 0.014 0.002 TRP F 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 ( 9248) covalent geometry : angle 0.71664 / 0.41 (13450) hydrogen bonds : bond 0.04971 / 3.36 ( 618) hydrogen bonds : angle 2.63130 / 1.90 ( 1559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8776 (ttmt) REVERT: A 55 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8135 (mtmm) REVERT: B 23 SER cc_start: 0.8788 (p) cc_final: 0.8503 (t) REVERT: F 64 LEU cc_start: 0.9393 (tp) cc_final: 0.9084 (mp) outliers start: 13 outliers final: 13 residues processed: 84 average time/residue: 0.1028 time to fit residues: 11.1327 Evaluate side-chains 80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN C 4 ASN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.170296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117257 restraints weight = 14099.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121592 restraints weight = 7519.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122246 restraints weight = 4743.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122707 restraints weight = 4373.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122974 restraints weight = 4082.500| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9248 Z= 0.194 Angle : 0.711 7.934 13450 Z= 0.409 Chirality : 0.049 0.355 1434 Planarity : 0.003 0.019 934 Dihedral : 32.536 171.804 3170 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.17 % Allowed : 16.67 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.36), residues: 528 helix: 2.92 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -0.83 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.010 0.001 TYR A 44 PHE 0.013 0.002 PHE D 5 TRP 0.011 0.002 TRP C 37 HIS 0.003 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 ( 9248) covalent geometry : angle 0.71104 / 0.41 (13450) hydrogen bonds : bond 0.05056 / 3.41 ( 618) hydrogen bonds : angle 2.78277 / 2.01 ( 1559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8823 (ttmt) REVERT: A 55 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8093 (mtmm) REVERT: B 23 SER cc_start: 0.8863 (p) cc_final: 0.8592 (t) REVERT: F 64 LEU cc_start: 0.9422 (tp) cc_final: 0.9087 (mp) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.1157 time to fit residues: 11.0023 Evaluate side-chains 76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 67 GLN E 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.168770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115149 restraints weight = 14109.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119251 restraints weight = 8396.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.120431 restraints weight = 5419.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120513 restraints weight = 4960.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120808 restraints weight = 4541.082| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9248 Z= 0.242 Angle : 0.739 8.333 13450 Z= 0.418 Chirality : 0.049 0.378 1434 Planarity : 0.004 0.030 934 Dihedral : 32.632 165.011 3170 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % Favored : 77.56 % 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: 3.17 (0.35), residues: 528 helix: 2.70 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.86 (0.54), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 50 TYR 0.004 0.001 TYR A 44 PHE 0.015 0.003 PHE D 5 TRP 0.010 0.002 TRP D 37 HIS 0.026 0.004 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 ( 9248) covalent geometry : angle 0.73890 / 0.42 (13450) hydrogen bonds : bond 0.05352 / 3.60 ( 618) hydrogen bonds : angle 3.00337 / 2.17 ( 1559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8875 (ttmt) REVERT: A 55 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8083 (mtmm) REVERT: F 56 THR cc_start: 0.9212 (m) cc_final: 0.8858 (p) outliers start: 14 outliers final: 13 residues processed: 76 average time/residue: 0.1077 time to fit residues: 10.5495 Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 30.0000 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 30.0000 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN E 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.170972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118412 restraints weight = 14127.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122423 restraints weight = 7339.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122983 restraints weight = 4803.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123494 restraints weight = 4482.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123736 restraints weight = 4167.958| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9248 Z= 0.163 Angle : 0.665 8.221 13450 Z= 0.388 Chirality : 0.046 0.350 1434 Planarity : 0.003 0.017 934 Dihedral : 32.526 158.012 3170 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.85 % Allowed : 18.91 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.67 (0.36), residues: 528 helix: 3.07 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.83 (0.54), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.007 0.001 TYR D 44 PHE 0.011 0.002 PHE D 5 TRP 0.011 0.002 TRP D 37 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 ( 9248) covalent geometry : angle 0.66508 / 0.39 (13450) hydrogen bonds : bond 0.04655 / 3.16 ( 618) hydrogen bonds : angle 2.66291 / 1.92 ( 1559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8850 (ttmt) REVERT: A 55 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8115 (mtmm) REVERT: F 56 THR cc_start: 0.9239 (m) cc_final: 0.8888 (p) REVERT: F 64 LEU cc_start: 0.9428 (tp) cc_final: 0.9063 (mp) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.0988 time to fit residues: 9.2158 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 40.0000 chunk 25 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.171176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.118506 restraints weight = 14224.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.122304 restraints weight = 7472.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124417 restraints weight = 5022.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124829 restraints weight = 3848.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.125305 restraints weight = 3821.147| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9248 Z= 0.141 Angle : 0.608 7.740 13450 Z= 0.365 Chirality : 0.042 0.255 1434 Planarity : 0.003 0.025 934 Dihedral : 32.228 148.490 3170 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 19.23 % Favored : 77.24 % 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: 4.21 (0.36), residues: 528 helix: 3.49 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.86 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 9 TYR 0.009 0.002 TYR D 44 PHE 0.008 0.002 PHE E 5 TRP 0.016 0.002 TRP D 37 HIS 0.001 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.14 ( 9248) covalent geometry : angle 0.60828 / 0.37 (13450) hydrogen bonds : bond 0.04363 / 2.98 ( 618) hydrogen bonds : angle 2.33619 / 1.68 ( 1559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8735 (ttmt) REVERT: A 55 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8091 (mtmm) REVERT: F 64 LEU cc_start: 0.9451 (tp) cc_final: 0.9078 (mp) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.1121 time to fit residues: 10.3179 Evaluate side-chains 73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN C 31 ASN D 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.170061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117905 restraints weight = 14177.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121775 restraints weight = 7277.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122601 restraints weight = 4667.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122985 restraints weight = 4332.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123287 restraints weight = 4030.298| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9248 Z= 0.154 Angle : 0.615 7.864 13450 Z= 0.365 Chirality : 0.042 0.276 1434 Planarity : 0.003 0.017 934 Dihedral : 32.257 150.433 3170 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.88 % Allowed : 19.87 % Favored : 77.24 % 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: 4.28 (0.36), residues: 528 helix: 3.54 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.83 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.006 0.001 TYR B 44 PHE 0.009 0.002 PHE D 5 TRP 0.013 0.002 TRP D 37 HIS 0.002 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 ( 9248) covalent geometry : angle 0.61499 / 0.37 (13450) hydrogen bonds : bond 0.04418 / 3.01 ( 618) hydrogen bonds : angle 2.38194 / 1.72 ( 1559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8787 (ttmt) REVERT: A 55 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8076 (mtmm) REVERT: F 64 LEU cc_start: 0.9453 (tp) cc_final: 0.9065 (mp) outliers start: 9 outliers final: 9 residues processed: 71 average time/residue: 0.0927 time to fit residues: 8.5760 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 58 optimal weight: 40.0000 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN D 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.170467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118500 restraints weight = 14132.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122781 restraints weight = 7339.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123451 restraints weight = 4684.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.123895 restraints weight = 4305.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124119 restraints weight = 4041.773| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9248 Z= 0.145 Angle : 0.610 7.934 13450 Z= 0.362 Chirality : 0.042 0.281 1434 Planarity : 0.003 0.024 934 Dihedral : 32.254 151.055 3170 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.49 % Allowed : 18.59 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.36), residues: 528 helix: 3.53 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.80 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 50 TYR 0.006 0.001 TYR C 44 PHE 0.008 0.002 PHE D 5 TRP 0.013 0.002 TRP D 37 HIS 0.002 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 ( 9248) covalent geometry : angle 0.60957 / 0.36 (13450) hydrogen bonds : bond 0.04339 / 2.96 ( 618) hydrogen bonds : angle 2.36522 / 1.71 ( 1559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8762 (ttmt) REVERT: A 55 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8092 (mtmm) REVERT: F 64 LEU cc_start: 0.9457 (tp) cc_final: 0.9068 (mp) outliers start: 14 outliers final: 13 residues processed: 74 average time/residue: 0.1019 time to fit residues: 9.8711 Evaluate side-chains 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 30.0000 chunk 60 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 GLN E 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.168566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114238 restraints weight = 14039.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118713 restraints weight = 7724.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120708 restraints weight = 4610.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.120526 restraints weight = 4131.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120881 restraints weight = 4029.863| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9248 Z= 0.296 Angle : 0.734 8.001 13450 Z= 0.412 Chirality : 0.046 0.288 1434 Planarity : 0.005 0.049 934 Dihedral : 32.483 151.182 3170 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 5.13 % Allowed : 17.95 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.36), residues: 528 helix: 2.98 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.78 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 15 TYR 0.003 0.001 TYR A 44 PHE 0.017 0.004 PHE D 5 TRP 0.014 0.002 TRP D 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.30 ( 9248) covalent geometry : angle 0.73353 / 0.41 (13450) hydrogen bonds : bond 0.05309 / 3.57 ( 618) hydrogen bonds : angle 2.95445 / 2.14 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.95 seconds wall clock time: 31 minutes 27.44 seconds (1887.44 seconds total)