Starting phenix.real_space_refine on Thu Jul 2 12:03:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv7_53388/07_2026/9qv7_53388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv7_53388/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qv7_53388/07_2026/9qv7_53388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv7_53388/07_2026/9qv7_53388.map" model { file = "/net/cci-nas-00/data/ceres_data/9qv7_53388/07_2026/9qv7_53388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv7_53388/07_2026/9qv7_53388.cif" } 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-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: 1.40, per 1000 atoms: 0.16 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 195.4 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 79.0% alpha, 2.9% beta 90 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 1.13 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: 1.20 Time building geometry restraints manager: 0.86 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: 10920 2.21 - 4.42: 1975 4.42 - 6.64: 502 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 1.50e+00 4.44e-01 5.44e+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: 14.770 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: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.780 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- 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 : 1.867 11.061 13450 Z= 1.230 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 1.86745 / 1.23 (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 : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.8242 (m-40) cc_final: 0.7910 (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: 0.6716 (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: 0.8530 (tt0) REVERT: B 60 ASN cc_start: 0.8065 (m-40) cc_final: 0.7762 (t0) REVERT: E 11 GLU cc_start: 0.8600 (tt0) cc_final: 0.7771 (tm-30) REVERT: E 15 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8086 (mtt90) REVERT: E 23 SER cc_start: 0.9262 (m) cc_final: 0.8917 (p) REVERT: F 56 THR cc_start: 0.8121 (m) cc_final: 0.7734 (p) outliers start: 3 outliers final: 0 residues processed: 118 average time/residue: 0.1208 time to fit residues: 17.5618 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 : 0.149 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 9.9990 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: 50.0000 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 6.3790 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.155081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092952 restraints weight = 18504.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096159 restraints weight = 9130.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098305 restraints weight = 6009.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099667 restraints weight = 4725.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100417 restraints weight = 4141.720| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9248 Z= 0.386 Angle : 1.034 10.858 13450 Z= 0.579 Chirality : 0.074 0.385 1434 Planarity : 0.006 0.078 934 Dihedral : 34.197 178.992 3170 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 2.24 % Allowed : 12.50 % Favored : 85.26 % 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: 1.69 (0.33), residues: 528 helix: 1.61 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 15 TYR 0.017 0.002 TYR D 44 PHE 0.021 0.004 PHE D 5 TRP 0.013 0.003 TRP C 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.39 ( 9248) covalent geometry : angle 1.03390 / 0.58 (13450) hydrogen bonds : bond 0.08812 / 6.00 ( 552) hydrogen bonds : angle 4.27071 / 3.07 ( 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 99 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9126 (tttt) cc_final: 0.8814 (tmmt) REVERT: A 37 TRP cc_start: 0.7803 (t60) cc_final: 0.7281 (t60) REVERT: B 4 ASN cc_start: 0.8719 (m110) cc_final: 0.7672 (t0) REVERT: B 11 GLU cc_start: 0.8903 (tt0) cc_final: 0.8665 (tt0) REVERT: B 21 ARG cc_start: 0.8623 (mtp85) cc_final: 0.7943 (mtp85) REVERT: F 61 ASP cc_start: 0.8855 (m-30) cc_final: 0.8627 (m-30) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.1071 time to fit residues: 12.9841 Evaluate side-chains 87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN C 51 HIS D 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.159657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097589 restraints weight = 18540.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101040 restraints weight = 8828.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103405 restraints weight = 5673.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104842 restraints weight = 4411.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105667 restraints weight = 3855.334| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9248 Z= 0.219 Angle : 0.811 8.009 13450 Z= 0.471 Chirality : 0.063 0.349 1434 Planarity : 0.005 0.045 934 Dihedral : 34.307 177.303 3170 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.24 % Allowed : 17.95 % Favored : 79.81 % 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: 3.12 (0.34), residues: 528 helix: 2.67 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.33 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 54 TYR 0.022 0.003 TYR A 44 PHE 0.014 0.003 PHE D 5 TRP 0.008 0.001 TRP A 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 ( 9248) covalent geometry : angle 0.81143 / 0.47 (13450) hydrogen bonds : bond 0.06846 / 4.63 ( 552) hydrogen bonds : angle 3.45353 / 2.47 ( 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 94 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9014 (tttt) cc_final: 0.8699 (tmmt) REVERT: A 37 TRP cc_start: 0.7800 (t60) cc_final: 0.7505 (t60) REVERT: A 55 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8531 (pttm) REVERT: B 4 ASN cc_start: 0.8638 (m110) cc_final: 0.7313 (t0) REVERT: B 30 MET cc_start: 0.8414 (tpt) cc_final: 0.7994 (tpt) REVERT: B 37 TRP cc_start: 0.8269 (t60) cc_final: 0.7680 (t60) REVERT: F 48 ILE cc_start: 0.8165 (tt) cc_final: 0.7905 (tt) REVERT: F 61 ASP cc_start: 0.8810 (m-30) cc_final: 0.8474 (m-30) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.1086 time to fit residues: 12.0789 Evaluate side-chains 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN 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: 0.6980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN E 20 GLN E 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.163188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101602 restraints weight = 18681.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105325 restraints weight = 8669.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107832 restraints weight = 5474.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109313 restraints weight = 4210.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110153 restraints weight = 3668.742| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9248 Z= 0.150 Angle : 0.738 7.758 13450 Z= 0.430 Chirality : 0.058 0.368 1434 Planarity : 0.004 0.044 934 Dihedral : 34.006 174.869 3170 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.92 % Allowed : 17.95 % 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: 3.97 (0.34), residues: 528 helix: 3.33 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.36 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 50 TYR 0.006 0.001 TYR D 44 PHE 0.008 0.002 PHE B 5 TRP 0.004 0.001 TRP D 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.15 ( 9248) covalent geometry : angle 0.73808 / 0.43 (13450) hydrogen bonds : bond 0.05939 / 4.08 ( 552) hydrogen bonds : angle 2.92242 / 2.08 ( 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 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8937 (tttt) cc_final: 0.8645 (tmmt) REVERT: A 55 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8400 (pttm) REVERT: B 36 ASP cc_start: 0.8809 (t0) cc_final: 0.8496 (t0) REVERT: B 37 TRP cc_start: 0.8244 (t60) cc_final: 0.7731 (t60) REVERT: C 43 LYS cc_start: 0.8271 (tppt) cc_final: 0.8018 (ttmm) REVERT: F 48 ILE cc_start: 0.8185 (tt) cc_final: 0.7913 (tt) REVERT: F 50 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8073 (tmm-80) outliers start: 6 outliers final: 2 residues processed: 92 average time/residue: 0.1183 time to fit residues: 13.5628 Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN 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: 40.0000 chunk 45 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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** F 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.159417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096586 restraints weight = 18258.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099798 restraints weight = 9171.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.101985 restraints weight = 6078.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103362 restraints weight = 4790.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104091 restraints weight = 4202.682| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9248 Z= 0.234 Angle : 0.759 7.561 13450 Z= 0.434 Chirality : 0.057 0.379 1434 Planarity : 0.004 0.033 934 Dihedral : 34.101 179.904 3170 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.24 % Allowed : 17.95 % Favored : 79.81 % 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: 3.46 (0.33), residues: 528 helix: 2.93 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.31 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 50 TYR 0.008 0.001 TYR D 44 PHE 0.009 0.002 PHE D 5 TRP 0.006 0.002 TRP F 37 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 ( 9248) covalent geometry : angle 0.75877 / 0.43 (13450) hydrogen bonds : bond 0.06396 / 4.39 ( 552) hydrogen bonds : angle 3.45043 / 2.48 ( 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 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8931 (tttt) cc_final: 0.8654 (tmmt) REVERT: A 37 TRP cc_start: 0.7872 (t60) cc_final: 0.6973 (t60) REVERT: A 55 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8295 (pttm) REVERT: B 4 ASN cc_start: 0.8656 (m110) cc_final: 0.7287 (t0) REVERT: B 36 ASP cc_start: 0.8813 (t0) cc_final: 0.8526 (t0) REVERT: F 58 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7803 (mttm) REVERT: F 61 ASP cc_start: 0.8790 (m-30) cc_final: 0.8357 (m-30) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1084 time to fit residues: 12.3248 Evaluate side-chains 92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 23 SER 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: 9.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN ** 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 = 0.4389 r_free = 0.4389 target = 0.160452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097922 restraints weight = 18245.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101155 restraints weight = 9104.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103440 restraints weight = 6020.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104829 restraints weight = 4715.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105653 restraints weight = 4123.788| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9248 Z= 0.188 Angle : 0.716 7.178 13450 Z= 0.413 Chirality : 0.054 0.371 1434 Planarity : 0.004 0.036 934 Dihedral : 34.048 178.879 3170 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % 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: 3.73 (0.34), residues: 528 helix: 3.29 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.66 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 50 TYR 0.005 0.001 TYR D 44 PHE 0.015 0.003 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 0.00364 / 0.19 ( 9248) covalent geometry : angle 0.71586 / 0.41 (13450) hydrogen bonds : bond 0.06091 / 4.21 ( 552) hydrogen bonds : angle 3.23589 / 2.31 ( 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 92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8904 (tttt) cc_final: 0.8633 (tmmt) REVERT: A 20 GLN cc_start: 0.8715 (mp10) cc_final: 0.8470 (mp10) REVERT: A 37 TRP cc_start: 0.7857 (t60) cc_final: 0.7188 (t60) REVERT: A 55 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8397 (mtmt) REVERT: B 30 MET cc_start: 0.8423 (tpt) cc_final: 0.8007 (tpt) REVERT: B 36 ASP cc_start: 0.8818 (t0) cc_final: 0.8538 (t0) REVERT: C 43 LYS cc_start: 0.8389 (tppt) cc_final: 0.8055 (ttmm) REVERT: E 41 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8174 (tt) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.1053 time to fit residues: 11.9411 Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 50.0000 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 40.0000 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 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 = 0.4414 r_free = 0.4414 target = 0.162455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100435 restraints weight = 18380.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103861 restraints weight = 9001.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106253 restraints weight = 5830.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.107692 restraints weight = 4528.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108601 restraints weight = 3955.489| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9248 Z= 0.141 Angle : 0.676 6.903 13450 Z= 0.394 Chirality : 0.052 0.357 1434 Planarity : 0.004 0.060 934 Dihedral : 33.977 178.083 3170 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.56 % Allowed : 18.91 % Favored : 78.53 % 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: 4.05 (0.34), residues: 528 helix: 3.51 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 50 TYR 0.004 0.001 TYR B 44 PHE 0.013 0.003 PHE D 5 TRP 0.006 0.001 TRP F 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 ( 9248) covalent geometry : angle 0.67552 / 0.39 (13450) hydrogen bonds : bond 0.05677 / 3.91 ( 552) hydrogen bonds : angle 2.94532 / 2.09 ( 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 87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8858 (tttt) cc_final: 0.8592 (tmmt) REVERT: A 20 GLN cc_start: 0.8702 (mp10) cc_final: 0.8460 (mp10) REVERT: A 37 TRP cc_start: 0.7834 (t60) cc_final: 0.7143 (t60) REVERT: B 21 ARG cc_start: 0.8640 (mtp85) cc_final: 0.7988 (mtp85) REVERT: B 36 ASP cc_start: 0.8804 (t0) cc_final: 0.8522 (t0) REVERT: C 43 LYS cc_start: 0.8352 (tppt) cc_final: 0.8032 (ttmm) REVERT: E 41 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8119 (tt) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.1131 time to fit residues: 12.2471 Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 VAL 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: 0.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** D 4 ASN ** 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 = 0.4379 r_free = 0.4379 target = 0.159708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103906 restraints weight = 18072.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.107932 restraints weight = 9778.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.107611 restraints weight = 6998.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107692 restraints weight = 5920.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108082 restraints weight = 5695.578| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9248 Z= 0.225 Angle : 0.715 6.957 13450 Z= 0.408 Chirality : 0.053 0.372 1434 Planarity : 0.003 0.027 934 Dihedral : 33.986 179.103 3170 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 3.75 (0.34), residues: 528 helix: 3.27 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 50 TYR 0.007 0.001 TYR D 44 PHE 0.013 0.003 PHE D 5 TRP 0.004 0.001 TRP F 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 ( 9248) covalent geometry : angle 0.71455 / 0.41 (13450) hydrogen bonds : bond 0.06134 / 4.19 ( 552) hydrogen bonds : angle 3.34106 / 2.38 ( 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 95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8912 (tttt) cc_final: 0.8663 (tmmt) REVERT: A 20 GLN cc_start: 0.8701 (mp10) cc_final: 0.8482 (mp10) REVERT: A 37 TRP cc_start: 0.7991 (t60) cc_final: 0.7293 (t60) REVERT: A 55 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8420 (pttm) REVERT: B 4 ASN cc_start: 0.8587 (m110) cc_final: 0.7353 (t0) REVERT: B 21 ARG cc_start: 0.8599 (mtp85) cc_final: 0.7973 (mtp85) REVERT: B 36 ASP cc_start: 0.8718 (t0) cc_final: 0.8460 (t0) REVERT: E 41 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8318 (tt) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.1091 time to fit residues: 12.5376 Evaluate side-chains 93 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 23 SER 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: 0.6980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 60 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN D 4 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.161187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098743 restraints weight = 18072.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102109 restraints weight = 9002.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104387 restraints weight = 5927.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105798 restraints weight = 4648.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106617 restraints weight = 4069.339| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9248 Z= 0.158 Angle : 0.674 7.052 13450 Z= 0.390 Chirality : 0.051 0.360 1434 Planarity : 0.004 0.057 934 Dihedral : 33.893 179.458 3170 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.85 % Allowed : 18.91 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.34), residues: 528 helix: 3.49 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.70 (0.45), 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 0.008 0.002 PHE B 5 TRP 0.006 0.001 TRP F 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 ( 9248) covalent geometry : angle 0.67380 / 0.39 (13450) hydrogen bonds : bond 0.05785 / 3.97 ( 552) hydrogen bonds : angle 3.09093 / 2.20 ( 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 96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8865 (tttt) cc_final: 0.8572 (tmmt) REVERT: A 20 GLN cc_start: 0.8733 (mp10) cc_final: 0.8491 (mp10) REVERT: A 37 TRP cc_start: 0.7874 (t60) cc_final: 0.7101 (t60) REVERT: B 4 ASN cc_start: 0.8642 (m110) cc_final: 0.7363 (t0) REVERT: B 36 ASP cc_start: 0.8811 (t0) cc_final: 0.8540 (t0) REVERT: C 43 LYS cc_start: 0.8387 (tppt) cc_final: 0.8024 (ttmm) REVERT: E 41 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8154 (tt) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.1124 time to fit residues: 13.1662 Evaluate side-chains 94 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 23 SER 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 18 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 58 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4400 r_free = 0.4400 target = 0.161372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105908 restraints weight = 18039.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.109828 restraints weight = 9749.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109637 restraints weight = 7012.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109733 restraints weight = 5897.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110193 restraints weight = 5656.283| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9248 Z= 0.165 Angle : 0.669 7.037 13450 Z= 0.388 Chirality : 0.050 0.358 1434 Planarity : 0.003 0.032 934 Dihedral : 33.814 179.232 3170 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.21 % Allowed : 18.27 % Favored : 78.53 % 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: 4.09 (0.34), residues: 528 helix: 3.55 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.70 (0.45), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 50 TYR 0.005 0.001 TYR B 44 PHE 0.012 0.003 PHE A 5 TRP 0.006 0.001 TRP F 37 HIS 0.001 0.000 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 9248) covalent geometry : angle 0.66898 / 0.39 (13450) hydrogen bonds : bond 0.05707 / 3.89 ( 552) hydrogen bonds : angle 3.07981 / 2.19 ( 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 95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8858 (tttt) cc_final: 0.8632 (tmmt) REVERT: A 20 GLN cc_start: 0.8678 (mp10) cc_final: 0.8472 (mp10) REVERT: A 37 TRP cc_start: 0.7968 (t60) cc_final: 0.7265 (t60) REVERT: A 55 LYS cc_start: 0.8668 (pttm) cc_final: 0.8400 (pttm) REVERT: B 30 MET cc_start: 0.8424 (tpt) cc_final: 0.8030 (tpt) REVERT: B 36 ASP cc_start: 0.8708 (t0) cc_final: 0.8456 (t0) REVERT: C 43 LYS cc_start: 0.8476 (tppt) cc_final: 0.8073 (ttmm) REVERT: E 41 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8278 (tt) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 0.1161 time to fit residues: 13.6502 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 : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 23 SER 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: 0.8980 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 57 optimal weight: 40.0000 chunk 60 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN 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 = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097240 restraints weight = 17292.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100333 restraints weight = 8478.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102397 restraints weight = 5573.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103663 restraints weight = 4391.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104327 restraints weight = 3858.768| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9248 Z= 0.256 Angle : 0.730 7.411 13450 Z= 0.414 Chirality : 0.052 0.378 1434 Planarity : 0.004 0.063 934 Dihedral : 33.800 179.630 3170 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.85 % Allowed : 17.95 % 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: 3.50 (0.34), residues: 528 helix: 3.07 (0.23), residues: 411 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 50 TYR 0.008 0.002 TYR B 44 PHE 0.014 0.003 PHE D 5 TRP 0.004 0.002 TRP B 37 HIS 0.002 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 ( 9248) covalent geometry : angle 0.72986 / 0.41 (13450) hydrogen bonds : bond 0.06583 / 4.47 ( 552) hydrogen bonds : angle 3.60250 / 2.57 ( 1429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.82 seconds wall clock time: 34 minutes 46.26 seconds (2086.26 seconds total)