Starting phenix.real_space_refine on Wed Aug 5 04:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv7_53388/08_2026/9qv7_53388.map" } resolution = 3.6 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= -0.001 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: 1.69, per 1000 atoms: 0.20 Number of scatterers: 8628 At special positions: 0 Unit cell: (147.825, 109.865, 109.865, 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: 0.66 Conformation dependent library (CDL) restraints added in 284.7 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 79.0% alpha, 2.9% beta 90 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.592A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 removed outlier: 3.514A pdb=" N GLY B 18 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 53 Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.589A pdb=" N ILE B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.502A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 53 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'D' and resid 6 through 18 Processing helix chain 'D' and resid 23 through 53 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 23 through 53 Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.611A pdb=" N LYS E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 23 through 53 Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'G' and resid 6 through 18 Processing helix chain 'G' and resid 23 through 53 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.553A pdb=" N LYS G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 23 through 53 Processing helix chain 'H' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 7.115A 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: 7.278A 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: 7.057A 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: 7.219A 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 57 331 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 221 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 183 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1388 1.33 - 1.45: 3201 1.45 - 1.57: 4157 1.57 - 1.69: 478 1.69 - 1.81: 24 Bond restraints: 9248 Sorted by residual: bond pdb=" P DG Y 106 " pdb=" O5' DG Y 106 " ideal model delta sigma weight residual 1.593 1.640 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" CA SER C 23 " pdb=" CB SER C 23 " ideal model delta sigma weight residual 1.529 1.458 0.070 1.53e-02 4.27e+03 2.12e+01 bond pdb=" CA SER D 23 " pdb=" CB SER D 23 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.48e-02 4.57e+03 1.79e+01 bond pdb=" P DA X 7 " pdb=" O5' DA X 7 " ideal model delta sigma weight residual 1.593 1.630 -0.037 1.00e-02 1.00e+04 1.35e+01 bond pdb=" P DG X 9 " pdb=" O5' DG X 9 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.27e+01 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 10884 2.21 - 4.42: 2006 4.42 - 6.64: 507 6.64 - 8.85: 50 8.85 - 11.06: 3 Bond angle restraints: 13450 Sorted by residual: angle pdb=" O3' DC X 67 " pdb=" P DC X 68 " pdb=" O5' DC X 68 " ideal model delta sigma weight residual 104.00 92.94 11.06 1.90e+00 2.77e-01 3.39e+01 angle pdb=" C4' DT X 74 " pdb=" O4' DT X 74 " pdb=" C1' DT X 74 " ideal model delta sigma weight residual 110.10 104.51 5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" O4' DG Y 110 " pdb=" C1' DG Y 110 " pdb=" N9 DG Y 110 " ideal model delta sigma weight residual 108.00 111.89 -3.89 7.00e-01 2.04e+00 3.08e+01 angle pdb=" CA ALA C 42 " pdb=" C ALA C 42 " pdb=" O ALA C 42 " ideal model delta sigma weight residual 120.42 114.86 5.56 1.06e+00 8.90e-01 2.75e+01 angle pdb=" O4' DA X 118 " pdb=" C1' DA X 118 " pdb=" N9 DA X 118 " ideal model delta sigma weight residual 108.00 111.62 -3.62 7.00e-01 2.04e+00 2.67e+01 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 3697 35.97 - 71.94: 977 71.94 - 107.90: 26 107.90 - 143.87: 0 143.87 - 179.84: 18 Dihedral angle restraints: 4718 sinusoidal: 3408 harmonic: 1310 Sorted by residual: dihedral pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " pdb=" CZ ARG B 21 " pdb=" NH1 ARG B 21 " ideal model delta sinusoidal sigma weight residual 0.00 84.98 -84.98 1 1.00e+01 1.00e-02 8.76e+01 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 81.94 -81.94 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CD ARG B 50 " pdb=" NE ARG B 50 " pdb=" CZ ARG B 50 " pdb=" NH1 ARG B 50 " ideal model delta sinusoidal sigma weight residual 0.00 80.03 -80.03 1 1.00e+01 1.00e-02 7.94e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1095 0.133 - 0.265: 101 0.265 - 0.398: 13 0.398 - 0.531: 164 0.531 - 0.663: 61 Chirality restraints: 1434 Sorted by residual: chirality pdb=" P DC X 29 " pdb=" OP1 DC X 29 " pdb=" OP2 DC X 29 " pdb=" O5' DC X 29 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P DC Y 20 " pdb=" OP1 DC Y 20 " pdb=" OP2 DC Y 20 " pdb=" O5' DC Y 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DG Y 83 " pdb=" OP1 DG Y 83 " pdb=" OP2 DG Y 83 " pdb=" O5' DG Y 83 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 9.93e+00 ... (remaining 1431 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 21 " -1.109 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG B 21 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 21 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 21 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 21 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 54 " -1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG F 54 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 54 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 54 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 54 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 50 " -1.058 9.50e-02 1.11e+02 4.74e-01 1.37e+02 pdb=" NE ARG B 50 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG B 50 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 50 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 50 " -0.014 2.00e-02 2.50e+03 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2904 2.92 - 3.42: 8499 3.42 - 3.91: 16761 3.91 - 4.41: 18856 4.41 - 4.90: 25024 Nonbonded interactions: 72044 Sorted by model distance: nonbonded pdb=" OE2 GLU C 47 " pdb=" NE2 HIS C 51 " model vdw 2.431 3.120 nonbonded pdb=" O5' DA Y 76 " pdb=" O4' DA Y 76 " model vdw 2.493 2.432 nonbonded pdb=" N ALA F 66 " pdb=" O ALA F 66 " model vdw 2.496 2.496 nonbonded pdb=" O5' DC X 40 " pdb=" O4' DC X 40 " model vdw 2.499 2.432 nonbonded pdb=" CA SER H 23 " pdb=" OP1 DG Y 106 " model vdw 2.538 3.470 ... (remaining 72039 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: 13.140 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: 1.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.014 0.070 9248 Z= 0.939 Angle : 1.876 11.061 13450 Z= 1.239 Chirality : 0.214 0.663 1434 Planarity : 0.043 0.497 934 Dihedral : 31.178 179.841 3950 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.96 % Allowed : 1.60 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.30), residues: 528 helix: -0.20 (0.22), residues: 416 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 50 TYR 0.018 0.003 TYR C 44 PHE 0.021 0.006 PHE A 5 TRP 0.026 0.010 TRP C 37 HIS 0.004 0.002 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01391 / 0.94 ( 9248) covalent geometry : angle 1.87615 / 1.24 (13450) hydrogen bonds : bond 0.21320 / 14.20 ( 552) hydrogen bonds : angle 8.50119 / 6.06 ( 1429) *********************** 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 120 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.8242 (m-40) cc_final: 0.7909 (m-40) REVERT: A 12 LYS cc_start: 0.9104 (tttt) cc_final: 0.8784 (tmmt) REVERT: A 37 TRP cc_start: 0.7621 (t60) cc_final: 0.6715 (t60) REVERT: B 4 ASN cc_start: 0.8634 (m110) cc_final: 0.7944 (m-40) REVERT: B 11 GLU cc_start: 0.8885 (tt0) cc_final: 0.8531 (tt0) REVERT: B 60 ASN cc_start: 0.8065 (m-40) cc_final: 0.7761 (t0) REVERT: E 11 GLU cc_start: 0.8600 (tt0) cc_final: 0.7768 (tm-30) REVERT: E 15 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8087 (mtt90) REVERT: E 23 SER cc_start: 0.9262 (m) cc_final: 0.8966 (p) outliers start: 3 outliers final: 0 residues processed: 118 average time/residue: 0.1570 time to fit residues: 22.7733 Evaluate side-chains 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 50.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.156211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096364 restraints weight = 18214.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099562 restraints weight = 8684.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101668 restraints weight = 5651.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102869 restraints weight = 4453.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103660 restraints weight = 3933.247| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9248 Z= 0.323 Angle : 1.015 10.344 13450 Z= 0.565 Chirality : 0.074 0.431 1434 Planarity : 0.008 0.119 934 Dihedral : 34.063 178.058 3170 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 2.24 % Allowed : 11.54 % 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: 1.85 (0.33), residues: 528 helix: 1.73 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.62 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 21 TYR 0.016 0.002 TYR D 44 PHE 0.018 0.004 PHE D 5 TRP 0.014 0.002 TRP C 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.32 ( 9248) covalent geometry : angle 1.01546 / 0.57 (13450) hydrogen bonds : bond 0.08333 / 5.68 ( 552) hydrogen bonds : angle 4.08822 / 2.93 ( 1429) *********************** 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 100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9108 (tttt) cc_final: 0.8803 (tmmt) REVERT: A 37 TRP cc_start: 0.7785 (t60) cc_final: 0.7277 (t60) REVERT: B 4 ASN cc_start: 0.8677 (m110) cc_final: 0.7619 (t0) REVERT: B 11 GLU cc_start: 0.8883 (tt0) cc_final: 0.8612 (tt0) REVERT: E 11 GLU cc_start: 0.8647 (tt0) cc_final: 0.8372 (tt0) REVERT: E 23 SER cc_start: 0.9266 (m) cc_final: 0.8944 (p) REVERT: F 61 ASP cc_start: 0.8829 (m-30) cc_final: 0.8618 (m-30) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.1383 time to fit residues: 16.6883 Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 HIS D 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.159272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097008 restraints weight = 18486.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100304 restraints weight = 8905.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102674 restraints weight = 5768.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104105 restraints weight = 4493.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104951 restraints weight = 3926.244| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9248 Z= 0.228 Angle : 0.837 8.409 13450 Z= 0.479 Chirality : 0.064 0.385 1434 Planarity : 0.005 0.038 934 Dihedral : 34.253 177.747 3170 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.24 % Allowed : 17.63 % 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: 3.01 (0.34), residues: 528 helix: 2.57 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.25 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 54 TYR 0.022 0.002 TYR A 44 PHE 0.016 0.003 PHE D 5 TRP 0.008 0.002 TRP A 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 ( 9248) covalent geometry : angle 0.83690 / 0.48 (13450) hydrogen bonds : bond 0.06820 / 4.61 ( 552) hydrogen bonds : angle 3.57533 / 2.56 ( 1429) *********************** 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 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.8817 (m-40) cc_final: 0.8554 (m-40) REVERT: A 12 LYS cc_start: 0.9027 (tttt) cc_final: 0.8719 (tmmt) REVERT: A 37 TRP cc_start: 0.7820 (t60) cc_final: 0.7509 (t60) REVERT: B 4 ASN cc_start: 0.8646 (m110) cc_final: 0.7360 (t0) REVERT: B 37 TRP cc_start: 0.8283 (t60) cc_final: 0.7650 (t60) REVERT: C 43 LYS cc_start: 0.8328 (tppt) cc_final: 0.8047 (ttmm) REVERT: F 56 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8332 (p) REVERT: F 61 ASP cc_start: 0.8824 (m-30) cc_final: 0.8538 (m-30) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.1443 time to fit residues: 16.0530 Evaluate side-chains 88 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN E 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.162674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.101815 restraints weight = 18661.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105232 restraints weight = 8859.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107654 restraints weight = 5652.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109130 restraints weight = 4370.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109930 restraints weight = 3812.845| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9248 Z= 0.157 Angle : 0.756 7.804 13450 Z= 0.435 Chirality : 0.060 0.393 1434 Planarity : 0.004 0.040 934 Dihedral : 33.928 174.531 3170 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.60 % Allowed : 17.95 % Favored : 80.45 % 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: 3.86 (0.35), residues: 528 helix: 3.26 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.39 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 50 TYR 0.005 0.001 TYR D 44 PHE 0.010 0.002 PHE A 5 TRP 0.003 0.001 TRP A 37 HIS 0.001 0.000 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.16 ( 9248) covalent geometry : angle 0.75622 / 0.44 (13450) hydrogen bonds : bond 0.06065 / 4.19 ( 552) hydrogen bonds : angle 2.97908 / 2.11 ( 1429) *********************** 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 95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8936 (tttt) cc_final: 0.8656 (tmmt) REVERT: A 37 TRP cc_start: 0.7741 (t60) cc_final: 0.7447 (t60) REVERT: A 55 LYS cc_start: 0.8695 (pttm) cc_final: 0.8383 (pttm) REVERT: B 21 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8131 (mtp85) REVERT: B 36 ASP cc_start: 0.8798 (t0) cc_final: 0.8493 (t0) REVERT: B 37 TRP cc_start: 0.8231 (t60) cc_final: 0.7692 (t60) REVERT: C 43 LYS cc_start: 0.8278 (tppt) cc_final: 0.8034 (ttmm) REVERT: F 48 ILE cc_start: 0.8185 (tt) cc_final: 0.7910 (tt) outliers start: 5 outliers final: 1 residues processed: 92 average time/residue: 0.1457 time to fit residues: 16.7710 Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN C 16 GLN D 4 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096031 restraints weight = 18361.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099228 restraints weight = 9238.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101375 restraints weight = 6111.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102808 restraints weight = 4827.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103590 restraints weight = 4227.984| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9248 Z= 0.258 Angle : 0.802 7.972 13450 Z= 0.451 Chirality : 0.059 0.404 1434 Planarity : 0.005 0.047 934 Dihedral : 34.013 179.506 3170 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.53 % Allowed : 17.63 % Favored : 78.85 % 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: 3.36 (0.34), residues: 528 helix: 2.86 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.33 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 50 TYR 0.009 0.001 TYR D 44 PHE 0.012 0.003 PHE D 5 TRP 0.004 0.001 TRP A 37 HIS 0.002 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 ( 9248) covalent geometry : angle 0.80228 / 0.45 (13450) hydrogen bonds : bond 0.06597 / 4.52 ( 552) hydrogen bonds : angle 3.59013 / 2.58 ( 1429) *********************** 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 100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8954 (tttt) cc_final: 0.8664 (tmmt) REVERT: A 37 TRP cc_start: 0.7880 (t60) cc_final: 0.6962 (t60) REVERT: B 4 ASN cc_start: 0.8680 (m110) cc_final: 0.7303 (t0) REVERT: B 36 ASP cc_start: 0.8822 (t0) cc_final: 0.8533 (t0) REVERT: F 58 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7887 (mttm) REVERT: F 61 ASP cc_start: 0.8838 (m-30) cc_final: 0.8450 (m-30) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.1429 time to fit residues: 16.4880 Evaluate side-chains 92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** E 20 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 = 0.4360 r_free = 0.4360 target = 0.158115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095084 restraints weight = 18221.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098187 restraints weight = 9325.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100349 restraints weight = 6226.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101691 restraints weight = 4919.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102437 restraints weight = 4318.902| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9248 Z= 0.278 Angle : 0.793 7.771 13450 Z= 0.445 Chirality : 0.058 0.416 1434 Planarity : 0.004 0.032 934 Dihedral : 34.025 178.872 3170 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.53 % Allowed : 19.87 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.34), residues: 528 helix: 2.84 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.68 (0.48), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 50 TYR 0.007 0.001 TYR D 44 PHE 0.014 0.004 PHE D 5 TRP 0.004 0.001 TRP C 37 HIS 0.002 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.28 ( 9248) covalent geometry : angle 0.79286 / 0.45 (13450) hydrogen bonds : bond 0.06688 / 4.62 ( 552) hydrogen bonds : angle 3.65180 / 2.61 ( 1429) *********************** 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 98 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8960 (tttt) cc_final: 0.8679 (tmmt) REVERT: A 20 GLN cc_start: 0.8761 (mp10) cc_final: 0.8224 (mp10) REVERT: A 37 TRP cc_start: 0.7897 (t60) cc_final: 0.7188 (t60) REVERT: B 36 ASP cc_start: 0.8827 (t0) cc_final: 0.8548 (t0) REVERT: C 43 LYS cc_start: 0.8440 (tppt) cc_final: 0.8094 (ttmm) REVERT: D 41 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8374 (tt) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1482 time to fit residues: 17.1014 Evaluate side-chains 95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 27 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 50.0000 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 40.0000 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN D 4 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.161820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099336 restraints weight = 18335.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102742 restraints weight = 9101.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105041 restraints weight = 5940.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106561 restraints weight = 4634.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107375 restraints weight = 4040.389| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9248 Z= 0.154 Angle : 0.703 8.108 13450 Z= 0.405 Chirality : 0.055 0.395 1434 Planarity : 0.004 0.053 934 Dihedral : 33.885 178.675 3170 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.28 % Allowed : 21.15 % 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: 3.92 (0.35), residues: 528 helix: 3.43 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.76 (0.46), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.004 0.001 TYR B 44 PHE 0.010 0.002 PHE D 5 TRP 0.006 0.001 TRP B 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 9248) covalent geometry : angle 0.70310 / 0.41 (13450) hydrogen bonds : bond 0.05837 / 4.02 ( 552) hydrogen bonds : angle 3.04873 / 2.16 ( 1429) *********************** 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 88 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8721 (mp10) cc_final: 0.8486 (mp10) REVERT: A 37 TRP cc_start: 0.7831 (t60) cc_final: 0.7142 (t60) REVERT: B 4 ASN cc_start: 0.8616 (m110) cc_final: 0.8128 (t0) REVERT: B 36 ASP cc_start: 0.8816 (t0) cc_final: 0.8539 (t0) REVERT: C 43 LYS cc_start: 0.8326 (tppt) cc_final: 0.8037 (ttmm) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.1438 time to fit residues: 15.5548 Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** E 20 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 = 0.4364 r_free = 0.4364 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094854 restraints weight = 18083.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098024 restraints weight = 9361.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100200 restraints weight = 6294.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101536 restraints weight = 4997.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.102290 restraints weight = 4400.391| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9248 Z= 0.264 Angle : 0.769 7.490 13450 Z= 0.430 Chirality : 0.056 0.413 1434 Planarity : 0.004 0.028 934 Dihedral : 33.889 177.642 3170 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % 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: 3.41 (0.34), residues: 528 helix: 3.02 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.69 (0.47), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 50 TYR 0.009 0.002 TYR D 44 PHE 0.013 0.003 PHE D 5 TRP 0.003 0.001 TRP D 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 ( 9248) covalent geometry : angle 0.76892 / 0.43 (13450) hydrogen bonds : bond 0.06668 / 4.53 ( 552) hydrogen bonds : angle 3.66090 / 2.62 ( 1429) *********************** 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 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8954 (tttt) cc_final: 0.8666 (tmmt) REVERT: A 20 GLN cc_start: 0.8777 (mp10) cc_final: 0.8534 (mp10) REVERT: A 37 TRP cc_start: 0.7924 (t60) cc_final: 0.7098 (t60) REVERT: B 4 ASN cc_start: 0.8731 (m110) cc_final: 0.7428 (t0) REVERT: B 36 ASP cc_start: 0.8816 (t0) cc_final: 0.8549 (t0) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.1208 time to fit residues: 14.0070 Evaluate side-chains 93 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 27 VAL 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: 0.8980 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 30.0000 chunk 60 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 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 = 0.4397 r_free = 0.4397 target = 0.161173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098343 restraints weight = 18102.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101611 restraints weight = 9130.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.103934 restraints weight = 6054.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105345 restraints weight = 4744.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106099 restraints weight = 4144.165| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9248 Z= 0.159 Angle : 0.690 7.285 13450 Z= 0.396 Chirality : 0.053 0.395 1434 Planarity : 0.003 0.045 934 Dihedral : 33.715 179.239 3170 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.92 % Allowed : 20.83 % 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: 4.01 (0.34), residues: 528 helix: 3.50 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.76 (0.46), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 50 TYR 0.005 0.001 TYR B 44 PHE 0.010 0.002 PHE D 5 TRP 0.005 0.001 TRP B 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 ( 9248) covalent geometry : angle 0.68958 / 0.40 (13450) hydrogen bonds : bond 0.05822 / 3.99 ( 552) hydrogen bonds : angle 3.13196 / 2.22 ( 1429) *********************** 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 90 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8901 (tttt) cc_final: 0.8593 (tmmt) REVERT: A 20 GLN cc_start: 0.8732 (mp10) cc_final: 0.8511 (mp10) REVERT: A 37 TRP cc_start: 0.7872 (t60) cc_final: 0.7109 (t60) REVERT: B 4 ASN cc_start: 0.8641 (m110) cc_final: 0.7303 (t0) REVERT: B 21 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8079 (mtp85) REVERT: B 36 ASP cc_start: 0.8811 (t0) cc_final: 0.8540 (t0) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.1190 time to fit residues: 13.1827 Evaluate side-chains 88 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 40.0000 chunk 58 optimal weight: 50.0000 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** E 20 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 = 0.4395 r_free = 0.4395 target = 0.160803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098003 restraints weight = 17998.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101292 restraints weight = 9165.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103575 restraints weight = 6090.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104955 restraints weight = 4788.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105692 restraints weight = 4195.278| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9248 Z= 0.174 Angle : 0.685 7.322 13450 Z= 0.391 Chirality : 0.051 0.391 1434 Planarity : 0.003 0.029 934 Dihedral : 33.599 179.992 3170 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.92 % Allowed : 21.79 % Favored : 76.28 % 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 (0.34), residues: 528 helix: 3.52 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.78 (0.45), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 50 TYR 0.005 0.001 TYR B 44 PHE 0.010 0.002 PHE D 5 TRP 0.005 0.001 TRP F 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 9248) covalent geometry : angle 0.68521 / 0.39 (13450) hydrogen bonds : bond 0.05745 / 3.89 ( 552) hydrogen bonds : angle 3.16597 / 2.25 ( 1429) ********************** 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 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8888 (tttt) cc_final: 0.8598 (tmmt) REVERT: A 20 GLN cc_start: 0.8743 (mp10) cc_final: 0.8526 (mp10) REVERT: A 37 TRP cc_start: 0.7892 (t60) cc_final: 0.7103 (t60) REVERT: A 55 LYS cc_start: 0.8399 (pttm) cc_final: 0.7877 (pttm) REVERT: B 4 ASN cc_start: 0.8652 (m110) cc_final: 0.7279 (t0) REVERT: B 36 ASP cc_start: 0.8801 (t0) cc_final: 0.8543 (t0) REVERT: C 43 LYS cc_start: 0.8453 (tppt) cc_final: 0.8033 (ttmm) outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.1206 time to fit residues: 13.6479 Evaluate side-chains 90 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 27 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 40.0000 chunk 57 optimal weight: 40.0000 chunk 60 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.157469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093566 restraints weight = 17940.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096565 restraints weight = 9424.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098675 restraints weight = 6422.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099979 restraints weight = 5111.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100676 restraints weight = 4497.062| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9248 Z= 0.321 Angle : 0.785 7.820 13450 Z= 0.439 Chirality : 0.055 0.415 1434 Planarity : 0.005 0.073 934 Dihedral : 33.710 179.122 3170 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.21 % Allowed : 20.19 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.34), residues: 528 helix: 2.73 (0.23), residues: 418 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 50 TYR 0.011 0.002 TYR A 44 PHE 0.015 0.003 PHE A 5 TRP 0.006 0.002 TRP C 37 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.32 ( 9248) covalent geometry : angle 0.78482 / 0.44 (13450) hydrogen bonds : bond 0.07012 / 4.76 ( 552) hydrogen bonds : angle 3.87240 / 2.76 ( 1429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.35 seconds wall clock time: 41 minutes 9.74 seconds (2469.74 seconds total)