Starting phenix.real_space_refine on Thu Jul 2 12:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv5_53386/07_2026/9qv5_53386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv5_53386/07_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_53386/07_2026/9qv5_53386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv5_53386/07_2026/9qv5_53386.map" model { file = "/net/cci-nas-00/data/ceres_data/9qv5_53386/07_2026/9qv5_53386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv5_53386/07_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-dev-6108/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: 1.29, per 1000 atoms: 0.15 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: 0.46 Conformation dependent library (CDL) restraints added in 256.9 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: 1.02 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: 1.14 Time building geometry restraints manager: 0.68 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: 9919 1.81 - 3.62: 2899 3.62 - 5.43: 573 5.43 - 7.23: 53 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: 24.680 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: 0.580 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.710 Find NCS groups from input model: 0.110 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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= 0.861 Angle : 1.688 9.044 13450 Z= 1.243 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 1.68770 / 1.24 (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 : 0.201 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: 0.8393 (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: 0.1012 time to fit residues: 11.6819 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 : 0.216 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 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 F 4 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.165312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.112092 restraints weight = 14482.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115182 restraints weight = 8501.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116844 restraints weight = 6087.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.117169 restraints weight = 5444.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.117209 restraints weight = 4884.335| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 9248 Z= 0.401 Angle : 1.079 9.845 13450 Z= 0.586 Chirality : 0.069 0.276 1434 Planarity : 0.009 0.105 934 Dihedral : 32.603 179.540 3170 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.21 % Allowed : 10.58 % Favored : 86.22 % 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: 0.53 (0.34), residues: 528 helix: 0.75 (0.24), 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 C 15 TYR 0.010 0.002 TYR A 44 PHE 0.018 0.004 PHE D 5 TRP 0.033 0.006 TRP C 37 HIS 0.008 0.002 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.40 ( 9248) covalent geometry : angle 1.07892 / 0.59 (13450) hydrogen bonds : bond 0.08204 / 5.41 ( 618) hydrogen bonds : angle 3.89449 / 2.83 ( 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 93 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.4311 (ttt) cc_final: 0.4107 (ttt) REVERT: D 30 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (tpt) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.1180 time to fit residues: 12.7829 Evaluate side-chains 87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 61 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 ASN 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 = 0.4363 r_free = 0.4363 target = 0.171227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117517 restraints weight = 14282.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.122518 restraints weight = 7033.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.123895 restraints weight = 4614.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124962 restraints weight = 3578.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125143 restraints weight = 3542.019| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9248 Z= 0.209 Angle : 0.743 8.862 13450 Z= 0.437 Chirality : 0.053 0.318 1434 Planarity : 0.004 0.061 934 Dihedral : 32.760 176.630 3170 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.85 % Allowed : 13.46 % Favored : 82.69 % 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: 2.25 (0.35), residues: 528 helix: 2.01 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -0.92 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.011 0.002 TYR A 44 PHE 0.016 0.003 PHE D 5 TRP 0.019 0.005 TRP F 37 HIS 0.003 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 ( 9248) covalent geometry : angle 0.74268 / 0.44 (13450) hydrogen bonds : bond 0.05588 / 3.76 ( 618) hydrogen bonds : angle 2.99115 / 2.16 ( 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 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8797 (ttmt) REVERT: A 16 GLN cc_start: 0.8324 (mm110) cc_final: 0.8081 (mm-40) REVERT: B 23 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 1 MET cc_start: 0.4443 (ttt) cc_final: 0.4232 (ttt) REVERT: F 64 LEU cc_start: 0.9392 (tp) cc_final: 0.9062 (mp) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.1112 time to fit residues: 11.1884 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 67 GLN 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 67 GLN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 ASN 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 = 0.4339 r_free = 0.4339 target = 0.169536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116339 restraints weight = 14285.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.120290 restraints weight = 7428.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121056 restraints weight = 4793.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121190 restraints weight = 4465.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121372 restraints weight = 4206.795| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9248 Z= 0.160 Angle : 0.688 8.043 13450 Z= 0.406 Chirality : 0.050 0.309 1434 Planarity : 0.003 0.026 934 Dihedral : 32.575 174.366 3170 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.21 % Allowed : 15.38 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.36), residues: 528 helix: 2.78 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -0.91 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 54 TYR 0.007 0.002 TYR A 44 PHE 0.010 0.002 PHE D 5 TRP 0.011 0.003 TRP C 37 HIS 0.002 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.16 ( 9248) covalent geometry : angle 0.68754 / 0.41 (13450) hydrogen bonds : bond 0.04945 / 3.34 ( 618) hydrogen bonds : angle 2.63720 / 1.91 ( 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 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8835 (ttmt) REVERT: B 23 SER cc_start: 0.8855 (p) cc_final: 0.8531 (t) REVERT: C 1 MET cc_start: 0.4582 (ttt) cc_final: 0.4348 (ttt) REVERT: D 20 GLN cc_start: 0.7697 (mp10) cc_final: 0.7318 (mp10) REVERT: F 64 LEU cc_start: 0.9407 (tp) cc_final: 0.9086 (mp) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.1043 time to fit residues: 11.1527 Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 ASN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.172130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120187 restraints weight = 14165.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123935 restraints weight = 7755.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124612 restraints weight = 5158.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124919 restraints weight = 4744.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125240 restraints weight = 4436.520| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9248 Z= 0.159 Angle : 0.660 7.655 13450 Z= 0.391 Chirality : 0.047 0.338 1434 Planarity : 0.003 0.020 934 Dihedral : 32.552 169.535 3170 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.85 % Allowed : 16.03 % 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: 3.71 (0.36), residues: 528 helix: 3.10 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -0.84 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 50 TYR 0.006 0.002 TYR C 44 PHE 0.010 0.002 PHE D 5 TRP 0.010 0.002 TRP C 37 HIS 0.003 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.16 ( 9248) covalent geometry : angle 0.65965 / 0.39 (13450) hydrogen bonds : bond 0.04712 / 3.19 ( 618) hydrogen bonds : angle 2.56606 / 1.85 ( 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 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8819 (ttmt) REVERT: C 1 MET cc_start: 0.4639 (ttt) cc_final: 0.4426 (ttt) REVERT: F 64 LEU cc_start: 0.9365 (tp) cc_final: 0.9060 (mp) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.1219 time to fit residues: 11.1610 Evaluate side-chains 74 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain F residue 1 MET 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: 7.9990 chunk 46 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 ASN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 67 GLN E 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.168842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115309 restraints weight = 13983.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119396 restraints weight = 7340.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120000 restraints weight = 4759.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120244 restraints weight = 4436.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121153 restraints weight = 4158.141| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9248 Z= 0.238 Angle : 0.723 8.222 13450 Z= 0.413 Chirality : 0.048 0.341 1434 Planarity : 0.004 0.038 934 Dihedral : 32.743 159.372 3170 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 4.81 % Allowed : 18.27 % 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: 3.39 (0.35), residues: 528 helix: 2.83 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -0.67 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.008 0.001 TYR A 44 PHE 0.015 0.003 PHE D 5 TRP 0.010 0.002 TRP C 37 HIS 0.004 0.002 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 ( 9248) covalent geometry : angle 0.72269 / 0.41 (13450) hydrogen bonds : bond 0.05461 / 3.68 ( 618) hydrogen bonds : angle 2.97989 / 2.15 ( 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 88 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8852 (ttmt) REVERT: E 30 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7763 (ttm) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.1226 time to fit residues: 12.3490 Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 41 ILE 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 51 HIS Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 40.0000 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 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 = 0.4352 r_free = 0.4352 target = 0.170383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117119 restraints weight = 14211.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120848 restraints weight = 7647.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122422 restraints weight = 5363.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123787 restraints weight = 4198.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.123919 restraints weight = 4027.607| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9248 Z= 0.163 Angle : 0.650 7.941 13450 Z= 0.383 Chirality : 0.045 0.301 1434 Planarity : 0.003 0.020 934 Dihedral : 32.644 154.276 3170 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.21 % Allowed : 18.59 % Favored : 78.21 % 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: 3.70 (0.35), residues: 528 helix: 3.07 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.65 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 50 TYR 0.009 0.002 TYR A 44 PHE 0.011 0.002 PHE D 5 TRP 0.008 0.002 TRP C 37 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 ( 9248) covalent geometry : angle 0.64978 / 0.38 (13450) hydrogen bonds : bond 0.04668 / 3.17 ( 618) hydrogen bonds : angle 2.67542 / 1.93 ( 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 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8846 (ttmt) REVERT: F 64 LEU cc_start: 0.9429 (tp) cc_final: 0.9068 (mp) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.1155 time to fit residues: 10.6675 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS 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 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 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: 0.3980 chunk 27 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114934 restraints weight = 14095.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.118924 restraints weight = 7278.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120263 restraints weight = 4951.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122060 restraints weight = 3988.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122000 restraints weight = 3905.149| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9248 Z= 0.169 Angle : 0.632 7.355 13450 Z= 0.374 Chirality : 0.042 0.235 1434 Planarity : 0.004 0.052 934 Dihedral : 32.510 148.017 3170 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.17 % Allowed : 17.63 % Favored : 78.21 % 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: 3.94 (0.35), residues: 528 helix: 3.25 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.67 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 50 TYR 0.006 0.001 TYR B 44 PHE 0.010 0.002 PHE D 5 TRP 0.009 0.002 TRP D 37 HIS 0.010 0.002 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 ( 9248) covalent geometry : angle 0.63232 / 0.37 (13450) hydrogen bonds : bond 0.04673 / 3.19 ( 618) hydrogen bonds : angle 2.59399 / 1.87 ( 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 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8779 (ttmt) REVERT: E 30 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7715 (ttm) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1227 time to fit residues: 11.2809 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 : 0.219 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 50.0000 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 59 optimal weight: 50.0000 chunk 10 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.168696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115056 restraints weight = 14210.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118605 restraints weight = 7584.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120741 restraints weight = 5158.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121079 restraints weight = 4013.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121325 restraints weight = 3975.007| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9248 Z= 0.164 Angle : 0.622 7.290 13450 Z= 0.369 Chirality : 0.042 0.247 1434 Planarity : 0.003 0.015 934 Dihedral : 32.503 149.314 3170 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % 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: 3.98 (0.36), residues: 528 helix: 3.28 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.66 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 50 TYR 0.007 0.001 TYR A 44 PHE 0.010 0.002 PHE D 5 TRP 0.013 0.002 TRP D 37 HIS 0.002 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 ( 9248) covalent geometry : angle 0.62191 / 0.37 (13450) hydrogen bonds : bond 0.04549 / 3.10 ( 618) hydrogen bonds : angle 2.55589 / 1.84 ( 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 76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8734 (ttmt) REVERT: E 30 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7737 (ttm) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1127 time to fit residues: 10.1349 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 : 0.197 ------------------------------------------------------------------------------- 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 55 LYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 40.0000 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115074 restraints weight = 14077.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119032 restraints weight = 7259.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120730 restraints weight = 4963.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.121181 restraints weight = 3931.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121416 restraints weight = 3908.294| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9248 Z= 0.156 Angle : 0.612 7.349 13450 Z= 0.364 Chirality : 0.041 0.253 1434 Planarity : 0.003 0.013 934 Dihedral : 32.476 150.165 3170 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 4.02 (0.36), residues: 528 helix: 3.31 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.70 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 50 TYR 0.007 0.001 TYR A 44 PHE 0.010 0.002 PHE D 5 TRP 0.014 0.002 TRP D 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 ( 9248) covalent geometry : angle 0.61197 / 0.36 (13450) hydrogen bonds : bond 0.04468 / 3.05 ( 618) hydrogen bonds : angle 2.51631 / 1.81 ( 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 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8752 (ttmt) REVERT: E 30 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7727 (ttm) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.1203 time to fit residues: 10.8029 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 : 0.211 ------------------------------------------------------------------------------- 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 55 LYS Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.0570 chunk 39 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 overall best weight: 2.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.165555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111522 restraints weight = 14140.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115603 restraints weight = 7608.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116216 restraints weight = 4855.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116552 restraints weight = 4477.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116670 restraints weight = 4251.055| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9248 Z= 0.283 Angle : 0.712 7.626 13450 Z= 0.405 Chirality : 0.044 0.259 1434 Planarity : 0.005 0.044 934 Dihedral : 32.630 150.434 3170 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.53 % Allowed : 18.91 % 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: 3.41 (0.35), residues: 528 helix: 2.88 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -0.87 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 50 TYR 0.008 0.001 TYR A 44 PHE 0.016 0.003 PHE D 5 TRP 0.015 0.002 TRP D 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.28 ( 9248) covalent geometry : angle 0.71235 / 0.41 (13450) hydrogen bonds : bond 0.05207 / 3.51 ( 618) hydrogen bonds : angle 2.96646 / 2.15 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.23 seconds wall clock time: 33 minutes 17.37 seconds (1997.37 seconds total)