Starting phenix.real_space_refine on Thu Jul 2 01:19:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yr7_34048/07_2026/7yr7_34048.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 12 5.16 5 C 2731 2.51 5 N 955 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 5102 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 36} Link IDs: {'rna2p': 23, 'rna3p': 94} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 0.87, per 1000 atoms: 0.17 Number of scatterers: 5102 At special positions: 0 Unit cell: (95.2, 84.15, 112.2, 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 118 15.00 O 1286 8.00 N 955 7.00 C 2731 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: 0.25 Conformation dependent library (CDL) restraints added in 61.8 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 17.9% alpha, 16.1% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'F' and resid 46 through 55 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'G' and resid 46 through 55 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'D' and resid 45 through 55 Processing sheet with id=AA1, first strand: chain 'F' and resid 20 through 26 removed outlier: 5.091A pdb=" N ARG F 31 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL F 25 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.336A pdb=" N LEU E 4 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G 32 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 20 through 26 removed outlier: 4.545A pdb=" N ARG E 31 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL E 25 " --> pdb=" O GLN E 29 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN E 29 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 6 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU G 4 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26 removed outlier: 5.224A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL B 25 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 32 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.602A pdb=" N LYS C 26 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 26 removed outlier: 5.564A pdb=" N VAL D 22 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY D 33 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY D 24 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 29 " --> pdb=" O LYS D 26 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1154 1.34 - 1.45: 1659 1.45 - 1.57: 2349 1.57 - 1.69: 235 1.69 - 1.81: 24 Bond restraints: 5421 Sorted by residual: bond pdb=" O3' A A 89 " pdb=" P G A 90 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.34e+01 bond pdb=" O3' G A 50 " pdb=" P G A 51 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" O3' C A 62 " pdb=" P A A 63 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.13e+01 bond pdb=" O3' C A 6 " pdb=" P A A 7 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 bond pdb=" O3' A A 36 " pdb=" P A A 37 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.72e+00 ... (remaining 5416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 7187 2.09 - 4.18: 619 4.18 - 6.27: 86 6.27 - 8.36: 14 8.36 - 10.45: 6 Bond angle restraints: 7912 Sorted by residual: angle pdb=" N VAL G 18 " pdb=" CA VAL G 18 " pdb=" C VAL G 18 " ideal model delta sigma weight residual 113.71 107.11 6.60 9.50e-01 1.11e+00 4.83e+01 angle pdb=" O3' C A 76 " pdb=" C3' C A 76 " pdb=" C2' C A 76 " ideal model delta sigma weight residual 109.50 99.30 10.20 1.50e+00 4.44e-01 4.63e+01 angle pdb=" C4' A A 78 " pdb=" C3' A A 78 " pdb=" O3' A A 78 " ideal model delta sigma weight residual 113.00 122.87 -9.87 1.50e+00 4.44e-01 4.33e+01 angle pdb=" C4' A A 75 " pdb=" C3' A A 75 " pdb=" O3' A A 75 " ideal model delta sigma weight residual 113.00 104.18 8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" N THR D 19 " pdb=" CA THR D 19 " pdb=" C THR D 19 " ideal model delta sigma weight residual 111.02 118.12 -7.10 1.25e+00 6.40e-01 3.23e+01 ... (remaining 7907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 2756 34.32 - 68.63: 218 68.63 - 102.95: 26 102.95 - 137.27: 1 137.27 - 171.58: 2 Dihedral angle restraints: 3003 sinusoidal: 2075 harmonic: 928 Sorted by residual: dihedral pdb=" O4' C A 62 " pdb=" C1' C A 62 " pdb=" N1 C A 62 " pdb=" C2 C A 62 " ideal model delta sinusoidal sigma weight residual 232.00 60.42 171.58 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C THR D 19 " pdb=" N THR D 19 " pdb=" CA THR D 19 " pdb=" CB THR D 19 " ideal model delta harmonic sigma weight residual -122.00 -135.66 13.66 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" CA LEU G 2 " pdb=" C LEU G 2 " pdb=" N ILE G 3 " pdb=" CA ILE G 3 " ideal model delta harmonic sigma weight residual -180.00 -152.76 -27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 3000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 791 0.100 - 0.200: 176 0.200 - 0.300: 42 0.300 - 0.400: 10 0.400 - 0.500: 1 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CA THR D 19 " pdb=" N THR D 19 " pdb=" C THR D 19 " pdb=" CB THR D 19 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" P G A 79 " pdb=" OP1 G A 79 " pdb=" OP2 G A 79 " pdb=" O5' G A 79 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE E 3 " pdb=" CA ILE E 3 " pdb=" CG1 ILE E 3 " pdb=" CG2 ILE E 3 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1017 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 47 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C ILE E 47 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE E 47 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR E 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 3 " 0.009 2.00e-02 2.50e+03 1.52e-02 6.94e+00 pdb=" N9 G A 3 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G A 3 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G A 3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 3 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G A 3 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G A 3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G A 3 " -0.039 2.00e-02 2.50e+03 pdb=" C2 G A 3 " 0.013 2.00e-02 2.50e+03 pdb=" N2 G A 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 36 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO F 37 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 37 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 37 " 0.036 5.00e-02 4.00e+02 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1653 2.89 - 3.39: 4213 3.39 - 3.89: 9409 3.89 - 4.40: 9604 4.40 - 4.90: 13814 Nonbonded interactions: 38693 Sorted by model distance: nonbonded pdb=" OG1 THR G 21 " pdb=" O GLY G 33 " model vdw 2.385 3.040 nonbonded pdb=" O5' A A 49 " pdb=" O4' A A 49 " model vdw 2.438 2.432 nonbonded pdb=" O THR E 5 " pdb=" OG1 THR E 5 " model vdw 2.445 3.040 nonbonded pdb=" O5' C A 6 " pdb=" O4' C A 6 " model vdw 2.447 2.432 nonbonded pdb=" N2 G A 40 " pdb=" O ALA D 36 " model vdw 2.448 3.120 ... (remaining 38688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 or (resid 26 and (name N or na \ me CA or name C or name O or name CB )) or resid 27 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) selection = (chain 'F' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'G' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 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 : 0.008 0.055 5421 Z= 0.463 Angle : 1.253 10.451 7912 Z= 0.759 Chirality : 0.094 0.500 1020 Planarity : 0.008 0.065 561 Dihedral : 21.393 171.582 2405 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.74 % Allowed : 12.77 % Favored : 82.48 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.35), residues: 318 helix: -4.63 (0.31), residues: 54 sheet: -4.54 (0.75), residues: 20 loop : -3.53 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 6 TYR 0.023 0.003 TYR E 48 HIS 0.006 0.002 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.46 ( 5421) covalent geometry : angle 1.25284 / 0.76 ( 7912) hydrogen bonds : bond 0.22230 / 14.83 ( 122) hydrogen bonds : angle 9.10100 / 6.24 ( 277) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7741 (mtt180) REVERT: E 55 LYS cc_start: 0.7684 (mttt) cc_final: 0.7199 (mttt) REVERT: B 7 ARG cc_start: 0.6979 (ptp90) cc_final: 0.6373 (ttm170) REVERT: B 31 ARG cc_start: 0.7764 (ttt180) cc_final: 0.7312 (mmm-85) REVERT: C 13 MET cc_start: 0.1168 (mtm) cc_final: 0.0761 (mpp) REVERT: C 42 VAL cc_start: 0.8757 (t) cc_final: 0.8528 (m) REVERT: D 10 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5930 (mm-30) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.0707 time to fit residues: 9.7177 Evaluate side-chains 91 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 28 ASN F 29 GLN B 35 ASN B 43 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.181884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.146073 restraints weight = 13797.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.149511 restraints weight = 8785.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151774 restraints weight = 6424.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153349 restraints weight = 5174.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.154503 restraints weight = 4429.673| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5421 Z= 0.244 Angle : 0.822 9.331 7912 Z= 0.426 Chirality : 0.048 0.223 1020 Planarity : 0.006 0.061 561 Dihedral : 20.803 174.239 1785 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.07 % Favored : 78.93 % Rotamer: Outliers : 5.47 % Allowed : 22.99 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.73 (0.40), residues: 318 helix: -3.02 (0.50), residues: 55 sheet: -4.50 (0.61), residues: 30 loop : -3.24 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 6 TYR 0.015 0.002 TYR E 48 HIS 0.008 0.002 HIS F 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 ( 5421) covalent geometry : angle 0.82176 / 0.43 ( 7912) hydrogen bonds : bond 0.08399 / 5.48 ( 122) hydrogen bonds : angle 5.55193 / 3.72 ( 277) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 LYS cc_start: 0.7817 (mttt) cc_final: 0.7287 (mttt) REVERT: B 1 MET cc_start: 0.7641 (ptm) cc_final: 0.7390 (ptm) REVERT: B 7 ARG cc_start: 0.6921 (ptp90) cc_final: 0.6498 (ttm170) REVERT: B 13 MET cc_start: 0.3680 (ttt) cc_final: 0.2267 (tmm) REVERT: B 31 ARG cc_start: 0.7641 (ttt180) cc_final: 0.7373 (mtp180) REVERT: B 49 GLN cc_start: 0.7594 (tp40) cc_final: 0.7128 (tp40) REVERT: C 35 ASN cc_start: 0.7906 (t0) cc_final: 0.7571 (m-40) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.0719 time to fit residues: 9.4185 Evaluate side-chains 100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 29 GLN G 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.182590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146982 restraints weight = 13581.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.150718 restraints weight = 8375.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.153252 restraints weight = 6003.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.154984 restraints weight = 4736.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156215 restraints weight = 3993.312| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5421 Z= 0.163 Angle : 0.686 8.163 7912 Z= 0.352 Chirality : 0.043 0.173 1020 Planarity : 0.005 0.037 561 Dihedral : 20.265 178.489 1781 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.92 % Favored : 82.08 % Rotamer: Outliers : 6.57 % Allowed : 27.74 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.96 (0.42), residues: 318 helix: -2.23 (0.53), residues: 55 sheet: -3.21 (1.34), residues: 10 loop : -2.98 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 6 TYR 0.012 0.002 TYR E 48 HIS 0.007 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 5421) covalent geometry : angle 0.68610 / 0.35 ( 7912) hydrogen bonds : bond 0.06806 / 4.22 ( 122) hydrogen bonds : angle 4.83272 / 3.21 ( 277) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8706 (mt0) cc_final: 0.8482 (mt0) REVERT: E 6 ARG cc_start: 0.6701 (mmt180) cc_final: 0.6019 (mmt180) REVERT: E 55 LYS cc_start: 0.7687 (mttt) cc_final: 0.7131 (mttt) REVERT: G 44 ARG cc_start: 0.7360 (ptt-90) cc_final: 0.6997 (ptt-90) REVERT: B 7 ARG cc_start: 0.6885 (ptp90) cc_final: 0.6336 (ttt90) REVERT: B 31 ARG cc_start: 0.7523 (ttt180) cc_final: 0.7312 (mtp180) REVERT: B 49 GLN cc_start: 0.7660 (tp40) cc_final: 0.7322 (tp40) REVERT: C 2 LEU cc_start: 0.8666 (tt) cc_final: 0.8437 (tt) REVERT: C 35 ASN cc_start: 0.7785 (t0) cc_final: 0.7497 (m-40) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.0698 time to fit residues: 9.1263 Evaluate side-chains 100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.0170 chunk 18 optimal weight: 4.9990 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 35 ASN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146971 restraints weight = 13800.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.150740 restraints weight = 8407.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.153291 restraints weight = 6011.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.155083 restraints weight = 4743.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.156297 restraints weight = 3990.595| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5421 Z= 0.148 Angle : 0.644 8.533 7912 Z= 0.329 Chirality : 0.041 0.160 1020 Planarity : 0.004 0.031 561 Dihedral : 20.123 176.181 1779 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 6.57 % Allowed : 29.56 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.55 (0.45), residues: 318 helix: -1.82 (0.59), residues: 55 sheet: -2.71 (1.53), residues: 10 loop : -2.72 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 6 TYR 0.010 0.001 TYR E 48 HIS 0.007 0.002 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 5421) covalent geometry : angle 0.64364 / 0.33 ( 7912) hydrogen bonds : bond 0.06508 / 4.06 ( 122) hydrogen bonds : angle 4.60727 / 3.05 ( 277) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 LYS cc_start: 0.7455 (mttt) cc_final: 0.6975 (mttt) REVERT: G 31 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6841 (mtp180) REVERT: G 44 ARG cc_start: 0.7694 (ptt-90) cc_final: 0.7018 (ptt-90) REVERT: B 7 ARG cc_start: 0.6922 (ptp90) cc_final: 0.6353 (ttt180) REVERT: B 31 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7177 (mtp180) REVERT: B 46 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6992 (pt0) REVERT: B 49 GLN cc_start: 0.7670 (tp40) cc_final: 0.7369 (tp40) REVERT: C 1 MET cc_start: 0.8610 (pmm) cc_final: 0.7951 (pmm) REVERT: C 35 ASN cc_start: 0.7889 (t0) cc_final: 0.7599 (m-40) outliers start: 18 outliers final: 13 residues processed: 102 average time/residue: 0.0743 time to fit residues: 9.3287 Evaluate side-chains 97 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.186038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.150760 restraints weight = 14041.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.154596 restraints weight = 8394.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.157189 restraints weight = 5977.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.159094 restraints weight = 4708.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.160455 restraints weight = 3951.185| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5421 Z= 0.114 Angle : 0.591 7.908 7912 Z= 0.297 Chirality : 0.039 0.145 1020 Planarity : 0.005 0.066 561 Dihedral : 19.719 177.702 1779 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 7.66 % Allowed : 29.93 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.24 (0.46), residues: 318 helix: -1.44 (0.62), residues: 55 sheet: -2.32 (1.68), residues: 10 loop : -2.55 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 6 TYR 0.010 0.001 TYR E 48 HIS 0.008 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 5421) covalent geometry : angle 0.59052 / 0.30 ( 7912) hydrogen bonds : bond 0.05716 / 3.55 ( 122) hydrogen bonds : angle 4.20643 / 2.77 ( 277) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 LYS cc_start: 0.7312 (mttt) cc_final: 0.6827 (mttt) REVERT: G 31 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6902 (mtp180) REVERT: G 44 ARG cc_start: 0.7344 (ptt-90) cc_final: 0.6681 (ptt-90) REVERT: G 45 GLU cc_start: 0.8072 (tp30) cc_final: 0.7130 (tm-30) REVERT: B 7 ARG cc_start: 0.6933 (ptp90) cc_final: 0.6360 (ttm-80) REVERT: B 31 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7279 (mtp180) REVERT: B 49 GLN cc_start: 0.7696 (tp40) cc_final: 0.7478 (tp40) REVERT: C 1 MET cc_start: 0.8439 (pmm) cc_final: 0.7009 (pmm) REVERT: C 35 ASN cc_start: 0.7917 (t0) cc_final: 0.7574 (m-40) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.0852 time to fit residues: 10.4407 Evaluate side-chains 94 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.185866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151656 restraints weight = 14212.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.155360 restraints weight = 8562.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157810 restraints weight = 6058.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.159713 restraints weight = 4774.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.161042 restraints weight = 3974.929| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5421 Z= 0.129 Angle : 0.628 8.389 7912 Z= 0.311 Chirality : 0.039 0.151 1020 Planarity : 0.005 0.064 561 Dihedral : 19.739 175.465 1779 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.18 % Favored : 80.82 % Rotamer: Outliers : 5.84 % Allowed : 29.56 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.08 (0.46), residues: 318 helix: -1.42 (0.63), residues: 55 sheet: -2.12 (1.75), residues: 10 loop : -2.41 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 6 TYR 0.013 0.001 TYR E 48 HIS 0.007 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 5421) covalent geometry : angle 0.62846 / 0.31 ( 7912) hydrogen bonds : bond 0.05979 / 3.78 ( 122) hydrogen bonds : angle 4.41534 / 2.95 ( 277) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.6195 (ttm) cc_final: 0.5706 (ttm) REVERT: E 55 LYS cc_start: 0.7430 (mttt) cc_final: 0.6942 (mttt) REVERT: G 31 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6945 (mtp180) REVERT: G 45 GLU cc_start: 0.8001 (tp30) cc_final: 0.7008 (tm-30) REVERT: B 7 ARG cc_start: 0.6991 (ptp90) cc_final: 0.6452 (ttm170) REVERT: B 44 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5149 (ttp-170) REVERT: B 49 GLN cc_start: 0.7823 (tp40) cc_final: 0.7524 (tp40) REVERT: C 1 MET cc_start: 0.8437 (pmm) cc_final: 0.6978 (pmm) REVERT: C 35 ASN cc_start: 0.7980 (t0) cc_final: 0.7686 (m-40) outliers start: 16 outliers final: 15 residues processed: 98 average time/residue: 0.0921 time to fit residues: 11.0476 Evaluate side-chains 98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.0970 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.176965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.140899 restraints weight = 13788.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.144400 restraints weight = 8549.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146951 restraints weight = 6186.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.148630 restraints weight = 4933.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149799 restraints weight = 4205.050| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5421 Z= 0.231 Angle : 0.798 10.909 7912 Z= 0.396 Chirality : 0.045 0.177 1020 Planarity : 0.006 0.090 561 Dihedral : 20.525 171.059 1779 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.07 % Favored : 78.93 % Rotamer: Outliers : 9.12 % Allowed : 27.01 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.45), residues: 318 helix: -1.85 (0.61), residues: 55 sheet: -3.80 (0.86), residues: 30 loop : -2.59 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 6 TYR 0.020 0.002 TYR E 48 HIS 0.008 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 ( 5421) covalent geometry : angle 0.79824 / 0.40 ( 7912) hydrogen bonds : bond 0.07698 / 5.05 ( 122) hydrogen bonds : angle 5.22215 / 3.56 ( 277) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.6045 (ttm) cc_final: 0.5563 (ttm) REVERT: E 55 LYS cc_start: 0.7633 (mttt) cc_final: 0.7116 (mttt) REVERT: G 31 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6939 (mtp180) REVERT: G 45 GLU cc_start: 0.8112 (tp30) cc_final: 0.7621 (tm-30) REVERT: B 1 MET cc_start: 0.7485 (ttt) cc_final: 0.6816 (ttt) REVERT: B 7 ARG cc_start: 0.7067 (ptp90) cc_final: 0.6462 (ttm170) REVERT: B 44 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5707 (ttp-170) REVERT: B 49 GLN cc_start: 0.7899 (tp40) cc_final: 0.7611 (tp40) REVERT: C 1 MET cc_start: 0.8454 (pmm) cc_final: 0.7083 (pmm) REVERT: C 35 ASN cc_start: 0.8015 (t0) cc_final: 0.7746 (m-40) outliers start: 25 outliers final: 18 residues processed: 107 average time/residue: 0.0877 time to fit residues: 11.6035 Evaluate side-chains 105 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 43 HIS ** 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 = 0.4471 r_free = 0.4471 target = 0.180615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.146217 restraints weight = 13779.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149642 restraints weight = 9103.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.152107 restraints weight = 6250.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.152870 restraints weight = 5444.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.153202 restraints weight = 4945.842| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5421 Z= 0.160 Angle : 0.717 9.685 7912 Z= 0.354 Chirality : 0.041 0.159 1020 Planarity : 0.006 0.116 561 Dihedral : 20.105 174.316 1779 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.24 % Favored : 81.76 % Rotamer: Outliers : 6.57 % Allowed : 29.56 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.21 (0.45), residues: 318 helix: -1.83 (0.60), residues: 55 sheet: None (None), residues: 0 loop : -2.44 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 6 TYR 0.015 0.002 TYR E 48 HIS 0.007 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 5421) covalent geometry : angle 0.71715 / 0.35 ( 7912) hydrogen bonds : bond 0.06597 / 4.29 ( 122) hydrogen bonds : angle 4.95829 / 3.35 ( 277) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6985 (mtp85) REVERT: E 1 MET cc_start: 0.5931 (ttm) cc_final: 0.5316 (ttm) REVERT: E 55 LYS cc_start: 0.7416 (mttt) cc_final: 0.6928 (mttt) REVERT: G 31 ARG cc_start: 0.7486 (mtp180) cc_final: 0.6949 (mtp180) REVERT: B 1 MET cc_start: 0.7577 (ttt) cc_final: 0.6771 (ttt) REVERT: B 7 ARG cc_start: 0.7028 (ptp90) cc_final: 0.6434 (ttm-80) REVERT: B 31 ARG cc_start: 0.7555 (ttt180) cc_final: 0.7283 (mtp180) REVERT: B 44 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5252 (ttp-170) REVERT: C 1 MET cc_start: 0.8218 (pmm) cc_final: 0.7045 (pmm) REVERT: C 35 ASN cc_start: 0.7959 (t0) cc_final: 0.7729 (m-40) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 0.0908 time to fit residues: 10.9291 Evaluate side-chains 96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 43 HIS ** 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 = 0.4473 r_free = 0.4473 target = 0.180400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145558 restraints weight = 13877.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.149310 restraints weight = 8326.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.151779 restraints weight = 5904.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.153537 restraints weight = 4660.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.154775 restraints weight = 3933.106| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5421 Z= 0.162 Angle : 0.713 9.289 7912 Z= 0.351 Chirality : 0.042 0.202 1020 Planarity : 0.005 0.036 561 Dihedral : 20.049 173.281 1775 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.44 % Favored : 79.56 % Rotamer: Outliers : 5.84 % Allowed : 29.93 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.31 (0.45), residues: 318 helix: -1.96 (0.58), residues: 55 sheet: -4.80 (1.05), residues: 10 loop : -2.35 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 6 TYR 0.015 0.002 TYR E 48 HIS 0.006 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 5421) covalent geometry : angle 0.71280 / 0.35 ( 7912) hydrogen bonds : bond 0.06615 / 4.30 ( 122) hydrogen bonds : angle 5.06869 / 3.41 ( 277) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6929 (mtp85) REVERT: E 1 MET cc_start: 0.5667 (ttm) cc_final: 0.5000 (ttm) REVERT: E 55 LYS cc_start: 0.7505 (mttt) cc_final: 0.6999 (mttt) REVERT: G 44 ARG cc_start: 0.7319 (ptt-90) cc_final: 0.6349 (ptt-90) REVERT: B 1 MET cc_start: 0.7641 (ttt) cc_final: 0.6940 (ttt) REVERT: B 7 ARG cc_start: 0.6976 (ptp90) cc_final: 0.6364 (ttm170) REVERT: B 31 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7242 (mtp180) REVERT: B 44 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5340 (ttp-170) REVERT: C 1 MET cc_start: 0.7935 (pmm) cc_final: 0.7035 (pmm) REVERT: C 13 MET cc_start: 0.1208 (mpp) cc_final: -0.0071 (mtm) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.0935 time to fit residues: 10.8370 Evaluate side-chains 94 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 43 HIS ** 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 = 0.4450 r_free = 0.4450 target = 0.179001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144320 restraints weight = 14078.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.148176 restraints weight = 8237.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150707 restraints weight = 5740.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.152417 restraints weight = 4499.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153618 restraints weight = 3774.411| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5421 Z= 0.175 Angle : 0.741 10.156 7912 Z= 0.365 Chirality : 0.043 0.204 1020 Planarity : 0.005 0.065 561 Dihedral : 20.145 172.392 1775 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.18 % Favored : 80.82 % Rotamer: Outliers : 5.47 % Allowed : 30.66 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.44 (0.44), residues: 318 helix: -2.02 (0.59), residues: 55 sheet: -4.93 (0.95), residues: 10 loop : -2.45 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 31 TYR 0.017 0.002 TYR E 48 HIS 0.006 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 5421) covalent geometry : angle 0.74143 / 0.36 ( 7912) hydrogen bonds : bond 0.06705 / 4.42 ( 122) hydrogen bonds : angle 5.09970 / 3.48 ( 277) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7542 (mtt180) cc_final: 0.6834 (mtp85) REVERT: E 1 MET cc_start: 0.5274 (ttm) cc_final: 0.4666 (ttm) REVERT: E 6 ARG cc_start: 0.7273 (tpp80) cc_final: 0.6997 (tpp80) REVERT: E 55 LYS cc_start: 0.7527 (mttt) cc_final: 0.7025 (mttt) REVERT: B 1 MET cc_start: 0.7587 (ttt) cc_final: 0.6932 (ttt) REVERT: B 7 ARG cc_start: 0.7047 (ptp90) cc_final: 0.6286 (ttm-80) REVERT: B 31 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7312 (mtp180) REVERT: B 44 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5201 (ttp-170) REVERT: B 49 GLN cc_start: 0.7793 (tp40) cc_final: 0.7495 (tp40) REVERT: C 1 MET cc_start: 0.7720 (pmm) cc_final: 0.6962 (pmm) REVERT: C 13 MET cc_start: 0.0993 (mpp) cc_final: -0.0126 (mtm) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.0847 time to fit residues: 9.9185 Evaluate side-chains 92 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 43 HIS ** 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 = 0.4469 r_free = 0.4469 target = 0.181498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.146905 restraints weight = 14111.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.150937 restraints weight = 8192.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.153655 restraints weight = 5660.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.155450 restraints weight = 4378.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.156700 restraints weight = 3635.632| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5421 Z= 0.140 Angle : 0.699 8.945 7912 Z= 0.342 Chirality : 0.041 0.195 1020 Planarity : 0.004 0.027 561 Dihedral : 19.844 175.020 1775 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 4.01 % Allowed : 32.12 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.29 (0.45), residues: 318 helix: -1.94 (0.57), residues: 55 sheet: -4.49 (1.24), residues: 10 loop : -2.35 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 6 TYR 0.014 0.001 TYR E 48 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 5421) covalent geometry : angle 0.69891 / 0.34 ( 7912) hydrogen bonds : bond 0.06224 / 4.07 ( 122) hydrogen bonds : angle 4.84391 / 3.23 ( 277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 999.65 seconds wall clock time: 17 minutes 48.54 seconds (1068.54 seconds total)