Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 15:59:23 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2d_9327/12_2021/6n2d_9327.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "b2 ARG 40": "NH1" <-> "NH2" Residue "b1 ARG 40": "NH1" <-> "NH2" Residue "a ARG 39": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "c0 ARG 36": "NH1" <-> "NH2" Residue "c2 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 72": "NH1" <-> "NH2" Residue "c4 ARG 36": "NH1" <-> "NH2" Residue "c5 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 36": "NH1" <-> "NH2" Residue "c7 ARG 36": "NH1" <-> "NH2" Residue "c8 ARG 29": "NH1" <-> "NH2" Residue "c8 ARG 36": "NH1" <-> "NH2" Residue "c9 ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7162 Number of models: 1 Model: "" Number of chains: 13 Chain: "b2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 286 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "b1" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 320 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 4.50, per 1000 atoms: 0.63 Number of scatterers: 7162 At special positions: 0 Unit cell: (72.08, 97.52, 76.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1213 8.00 N 1201 7.00 C 4727 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 - 3.50 Amimo acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'b2' and resid 10 through 29 Processing helix chain 'b2' and resid 29 through 43 Processing helix chain 'b1' and resid 9 through 49 removed outlier: 3.610A pdb=" N TYRb1 13 " --> pdb=" O GLYb1 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix Processing helix chain 'a' and resid 16 through 38 removed outlier: 3.582A pdb=" N MET a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 68 through 73 Processing helix chain 'a' and resid 75 through 92 removed outlier: 3.745A pdb=" N THR a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 130 Processing helix chain 'a' and resid 153 through 191 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 234 removed outlier: 4.263A pdb=" N MET a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'c0' and resid 3 through 37 Processing helix chain 'c0' and resid 40 through 72 removed outlier: 4.002A pdb=" N THRc0 47 " --> pdb=" O VALc0 43 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.923A pdb=" N PHEc0 67 " --> pdb=" O VALc0 63 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILEc0 68 " --> pdb=" O VALc0 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGc0 72 " --> pdb=" O ILEc0 68 " (cutoff:3.500A) Processing helix chain 'c1' and resid 3 through 37 Processing helix chain 'c1' and resid 40 through 72 removed outlier: 4.525A pdb=" N LEUc1 58 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) Proline residue: c1 59 - end of helix Processing helix chain 'c2' and resid 3 through 37 Processing helix chain 'c2' and resid 40 through 56 Processing helix chain 'c2' and resid 56 through 72 Processing helix chain 'c3' and resid 3 through 37 Processing helix chain 'c3' and resid 40 through 71 Proline residue: c3 59 - end of helix Processing helix chain 'c4' and resid 3 through 37 Processing helix chain 'c4' and resid 40 through 56 Processing helix chain 'c4' and resid 56 through 72 removed outlier: 4.032A pdb=" N ILEc4 68 " --> pdb=" O VALc4 64 " (cutoff:3.500A) Processing helix chain 'c5' and resid 3 through 37 Processing helix chain 'c5' and resid 40 through 72 removed outlier: 4.289A pdb=" N LEUc5 58 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 3 through 37 Processing helix chain 'c6' and resid 40 through 72 removed outlier: 4.373A pdb=" N LEUc6 58 " --> pdb=" O LEUc6 54 " (cutoff:3.500A) Proline residue: c6 59 - end of helix removed outlier: 3.635A pdb=" N GLYc6 71 " --> pdb=" O PHEc6 67 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGc6 72 " --> pdb=" O ILEc6 68 " (cutoff:3.500A) Processing helix chain 'c7' and resid 3 through 37 Processing helix chain 'c7' and resid 40 through 56 removed outlier: 3.665A pdb=" N LEUc7 44 " --> pdb=" O LEUc7 40 " (cutoff:3.500A) Processing helix chain 'c7' and resid 56 through 72 removed outlier: 3.504A pdb=" N ILEc7 60 " --> pdb=" O GLUc7 56 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 37 Processing helix chain 'c8' and resid 40 through 71 removed outlier: 4.938A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 3 through 37 removed outlier: 3.525A pdb=" N GLNc9 37 " --> pdb=" O GLYc9 33 " (cutoff:3.500A) Processing helix chain 'c9' and resid 40 through 71 removed outlier: 3.827A pdb=" N THRc9 47 " --> pdb=" O VALc9 43 " (cutoff:3.500A) Proline residue: c9 59 - end of helix 738 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 3.50 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: 2074 1.34 - 1.46: 1143 1.46 - 1.58: 4010 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 7268 Sorted by residual: bond pdb=" CG1 ILEc3 31 " pdb=" CD1 ILEc3 31 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 9.02e+00 bond pdb=" CG1 ILEc2 31 " pdb=" CD1 ILEc2 31 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.50e+00 bond pdb=" CG1 ILEc8 31 " pdb=" CD1 ILEc8 31 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.59e+00 bond pdb=" CG1 ILEc9 31 " pdb=" CD1 ILEc9 31 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.41e+00 bond pdb=" CG1 ILEc1 31 " pdb=" CD1 ILEc1 31 " ideal model delta sigma weight residual 1.513 1.419 0.094 3.90e-02 6.57e+02 5.83e+00 ... (remaining 7263 not shown) Histogram of bond angle deviations from ideal: 96.11 - 103.68: 85 103.68 - 111.26: 2760 111.26 - 118.83: 3216 118.83 - 126.40: 3765 126.40 - 133.97: 62 Bond angle restraints: 9888 Sorted by residual: angle pdb=" C SERc5 28 " pdb=" N ARGc5 29 " pdb=" CA ARGc5 29 " ideal model delta sigma weight residual 122.38 112.07 10.31 1.81e+00 3.05e-01 3.25e+01 angle pdb=" C ALAc0 57 " pdb=" N LEUc0 58 " pdb=" CA LEUc0 58 " ideal model delta sigma weight residual 121.80 111.35 10.45 2.44e+00 1.68e-01 1.83e+01 angle pdb=" N LEU a 76 " pdb=" CA LEU a 76 " pdb=" C LEU a 76 " ideal model delta sigma weight residual 111.28 115.74 -4.46 1.09e+00 8.42e-01 1.68e+01 angle pdb=" CA LEUc5 58 " pdb=" C LEUc5 58 " pdb=" N PROc5 59 " ideal model delta sigma weight residual 120.93 116.59 4.34 1.06e+00 8.90e-01 1.68e+01 angle pdb=" C ALAc3 57 " pdb=" N LEUc3 58 " pdb=" CA LEUc3 58 " ideal model delta sigma weight residual 121.80 111.88 9.92 2.44e+00 1.68e-01 1.65e+01 ... (remaining 9883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 3850 15.11 - 30.21: 259 30.21 - 45.32: 103 45.32 - 60.42: 4 60.42 - 75.53: 2 Dihedral angle restraints: 4218 sinusoidal: 1496 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ALAb2 29 " pdb=" C ALAb2 29 " pdb=" N TRPb2 30 " pdb=" CA TRPb2 30 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PHEb1 28 " pdb=" C PHEb1 28 " pdb=" N ALAb1 29 " pdb=" CA ALAb1 29 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TRPb2 30 " pdb=" C TRPb2 30 " pdb=" N GLNb2 31 " pdb=" CA GLNb2 31 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 912 0.066 - 0.132: 285 0.132 - 0.198: 58 0.198 - 0.264: 7 0.264 - 0.330: 4 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILEc9 10 " pdb=" CA ILEc9 10 " pdb=" CG1 ILEc9 10 " pdb=" CG2 ILEc9 10 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILEb1 11 " pdb=" CA ILEb1 11 " pdb=" CG1 ILEb1 11 " pdb=" CG2 ILEb1 11 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ARGc5 29 " pdb=" N ARGc5 29 " pdb=" C ARGc5 29 " pdb=" CB ARGc5 29 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1263 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUc1 58 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PROc1 59 " -0.133 5.00e-02 4.00e+02 pdb=" CA PROc1 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PROc1 59 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUc3 58 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PROc3 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROc3 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROc3 59 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLNc9 37 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PROc9 38 " -0.127 5.00e-02 4.00e+02 pdb=" CA PROc9 38 " 0.038 5.00e-02 4.00e+02 pdb=" CD PROc9 38 " 0.040 5.00e-02 4.00e+02 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 3 2.27 - 2.93: 2752 2.93 - 3.58: 11899 3.58 - 4.24: 16811 4.24 - 4.90: 28398 Nonbonded interactions: 59863 Sorted by model distance: nonbonded pdb=" O PHEc6 65 " pdb=" CD2 TYRc6 69 " model vdw 1.610 3.340 nonbonded pdb=" O LEU a 180 " pdb=" CD1 LEU a 184 " model vdw 1.633 3.460 nonbonded pdb=" O ALAc5 57 " pdb=" CD1 ILEc5 61 " model vdw 1.755 3.460 nonbonded pdb=" O VALc1 63 " pdb=" OG SERc1 66 " model vdw 2.280 2.440 nonbonded pdb=" O VALc3 63 " pdb=" OG SERc3 66 " model vdw 2.299 2.440 ... (remaining 59858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43)) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 43)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4727 2.51 5 N 1201 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Write .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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.370 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 22.750 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.190 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 0.117 7268 Z= 0.490 Angle : 1.207 11.420 9888 Z= 0.642 Chirality : 0.066 0.330 1266 Planarity : 0.010 0.077 1220 Dihedral : 11.746 75.526 2492 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.22), residues: 963 helix: -1.50 (0.14), residues: 892 sheet: None (None), residues: 0 loop : -3.52 (0.57), residues: 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 262 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 265 average time/residue: 0.2208 time to fit residues: 74.4971 Evaluate side-chains 208 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN a 16 ASN a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c4 45 GLN c5 23 ASN ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 23 ASN c9 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7268 Z= 0.264 Angle : 0.766 10.702 9888 Z= 0.388 Chirality : 0.044 0.214 1266 Planarity : 0.009 0.129 1220 Dihedral : 4.508 22.006 1043 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 7.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 963 helix: 0.36 (0.16), residues: 891 sheet: None (None), residues: 0 loop : -2.69 (0.66), residues: 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 0.841 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 260 average time/residue: 0.1914 time to fit residues: 65.1657 Evaluate side-chains 236 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0694 time to fit residues: 4.3933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7268 Z= 0.270 Angle : 0.759 9.946 9888 Z= 0.378 Chirality : 0.044 0.217 1266 Planarity : 0.008 0.110 1220 Dihedral : 4.365 22.598 1043 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 6.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 963 helix: 1.10 (0.17), residues: 892 sheet: None (None), residues: 0 loop : -2.16 (0.75), residues: 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 0.870 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 248 average time/residue: 0.1922 time to fit residues: 62.7406 Evaluate side-chains 223 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0664 time to fit residues: 3.0491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7268 Z= 0.267 Angle : 0.752 9.763 9888 Z= 0.372 Chirality : 0.044 0.211 1266 Planarity : 0.008 0.111 1220 Dihedral : 4.266 25.098 1043 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 5.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 963 helix: 1.38 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.98 (0.85), residues: 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 0.851 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 237 average time/residue: 0.1820 time to fit residues: 57.5973 Evaluate side-chains 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0746 time to fit residues: 3.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7268 Z= 0.262 Angle : 0.752 9.679 9888 Z= 0.373 Chirality : 0.044 0.207 1266 Planarity : 0.008 0.113 1220 Dihedral : 4.206 23.021 1043 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 963 helix: 1.50 (0.17), residues: 895 sheet: None (None), residues: 0 loop : -1.86 (0.85), residues: 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 0.872 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 242 average time/residue: 0.1953 time to fit residues: 62.0441 Evaluate side-chains 224 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0670 time to fit residues: 2.2025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 7268 Z= 0.280 Angle : 0.761 9.941 9888 Z= 0.378 Chirality : 0.044 0.210 1266 Planarity : 0.008 0.116 1220 Dihedral : 4.186 20.681 1043 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 963 helix: 1.55 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.86 (0.85), residues: 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 0.851 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 231 average time/residue: 0.1954 time to fit residues: 59.2819 Evaluate side-chains 223 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0711 time to fit residues: 2.6230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0970 chunk 53 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.0070 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7268 Z= 0.238 Angle : 0.734 9.165 9888 Z= 0.363 Chirality : 0.043 0.202 1266 Planarity : 0.008 0.122 1220 Dihedral : 4.174 19.328 1043 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.27), residues: 963 helix: 1.72 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.81 (0.86), residues: 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 0.899 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 225 average time/residue: 0.1983 time to fit residues: 58.5173 Evaluate side-chains 212 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1269 time to fit residues: 2.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 7268 Z= 0.309 Angle : 0.789 10.282 9888 Z= 0.398 Chirality : 0.045 0.222 1266 Planarity : 0.010 0.140 1220 Dihedral : 4.195 17.872 1043 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 963 helix: 1.59 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.80 (0.84), residues: 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 0.877 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 223 average time/residue: 0.2007 time to fit residues: 59.0416 Evaluate side-chains 221 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0830 time to fit residues: 2.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 7268 Z= 0.296 Angle : 0.791 9.673 9888 Z= 0.398 Chirality : 0.045 0.224 1266 Planarity : 0.010 0.117 1220 Dihedral : 4.228 16.680 1043 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 963 helix: 1.53 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.07 (0.77), residues: 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 0.823 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 221 average time/residue: 0.1916 time to fit residues: 55.8310 Evaluate side-chains 219 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 214 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0740 time to fit residues: 1.7513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.136 7268 Z= 0.303 Angle : 0.836 16.054 9888 Z= 0.427 Chirality : 0.046 0.239 1266 Planarity : 0.010 0.153 1220 Dihedral : 4.279 16.039 1043 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.26), residues: 963 helix: 1.46 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.24 (0.75), residues: 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 223 average time/residue: 0.1978 time to fit residues: 58.2383 Evaluate side-chains 218 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0697 time to fit residues: 1.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.0040 chunk 4 optimal weight: 1.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c6 37 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 = 0.4047 r_free = 0.4047 target = 0.155315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126206 restraints weight = 9070.629| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.06 r_work: 0.3679 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3659 rms_B_bonded: 1.92 restraints_weight: 0.1250 r_work: 0.3648 rms_B_bonded: 2.02 restraints_weight: 0.0625 r_work: 0.3636 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3623 rms_B_bonded: 2.32 restraints_weight: 0.0156 r_work: 0.3610 rms_B_bonded: 2.52 restraints_weight: 0.0078 r_work: 0.3595 rms_B_bonded: 2.75 restraints_weight: 0.0039 r_work: 0.3580 rms_B_bonded: 3.02 restraints_weight: 0.0020 r_work: 0.3563 rms_B_bonded: 3.32 restraints_weight: 0.0010 r_work: 0.3544 rms_B_bonded: 3.67 restraints_weight: 0.0005 r_work: 0.3524 rms_B_bonded: 4.06 restraints_weight: 0.0002 r_work: 0.3503 rms_B_bonded: 4.51 restraints_weight: 0.0001 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 7268 Z= 0.270 Angle : 0.813 12.097 9888 Z= 0.412 Chirality : 0.045 0.264 1266 Planarity : 0.010 0.132 1220 Dihedral : 4.274 19.104 1043 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 963 helix: 1.55 (0.17), residues: 895 sheet: None (None), residues: 0 loop : -2.16 (0.73), residues: 68 =============================================================================== Job complete usr+sys time: 1781.68 seconds wall clock time: 32 minutes 54.34 seconds (1974.34 seconds total)