Starting phenix.real_space_refine on Thu Mar 5 16:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.map" model { file = "/net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwx_20514/03_2026/6pwx_20514.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11964 atoms to isotropic. 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 292 5.49 5 S 27 5.16 5 C 8152 2.51 5 N 2673 2.21 5 O 3267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14411 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2447 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.07, per 1000 atoms: 0.21 Number of scatterers: 14411 At special positions: 0 Unit cell: (102.01, 129.28, 123.22, 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 27 16.00 P 292 15.00 O 3267 8.00 N 2673 7.00 C 8152 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: 1.34 Conformation dependent library (CDL) restraints added in 347.9 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 51.7% alpha, 12.1% beta 147 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 24 through 29 removed outlier: 4.311A pdb=" N GLN H 27 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.534A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.562A pdb=" N ASN I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 100 through 120 removed outlier: 3.685A pdb=" N ALA J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.484A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 101 through 121 removed outlier: 3.863A pdb=" N ALA N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.310A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.533A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.394A pdb=" N VAL A 318 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 309 " --> pdb=" O TRP A 303 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP A 303 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.652A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 7.102A pdb=" N ALA A 84 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 72 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 82 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP A 74 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 80 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP A 94 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 100 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115 removed outlier: 4.062A pdb=" N LYS A 112 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.976A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.142A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.050A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.169A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.382A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 77 through 78 479 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3042 1.33 - 1.45: 4521 1.45 - 1.57: 7085 1.57 - 1.69: 582 1.69 - 1.81: 41 Bond restraints: 15271 Sorted by residual: bond pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG ASP K 106 " pdb=" OD1 ASP K 106 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.41e+00 ... (remaining 15266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 21339 1.65 - 3.29: 541 3.29 - 4.94: 24 4.94 - 6.58: 7 6.58 - 8.23: 4 Bond angle restraints: 21915 Sorted by residual: angle pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " pdb=" CD GLU L 52 " ideal model delta sigma weight residual 112.60 118.76 -6.16 1.70e+00 3.46e-01 1.32e+01 angle pdb=" N ASP G 106 " pdb=" CA ASP G 106 " pdb=" CB ASP G 106 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.55e+00 4.16e-01 1.10e+01 ... (remaining 21910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.55: 6405 26.55 - 53.09: 1583 53.09 - 79.64: 404 79.64 - 106.18: 13 106.18 - 132.73: 3 Dihedral angle restraints: 8408 sinusoidal: 5295 harmonic: 3113 Sorted by residual: dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE H 50 " pdb=" C ILE H 50 " pdb=" N TYR H 51 " pdb=" CA TYR H 51 " ideal model delta harmonic sigma weight residual 180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DG P 94 " pdb=" C3' DG P 94 " pdb=" O3' DG P 94 " pdb=" P DG P 95 " ideal model delta sinusoidal sigma weight residual -140.00 -7.27 -132.73 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1634 0.028 - 0.057: 609 0.057 - 0.085: 165 0.085 - 0.113: 84 0.113 - 0.141: 17 Chirality restraints: 2509 Sorted by residual: chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL A 125 " pdb=" N VAL A 125 " pdb=" C VAL A 125 " pdb=" CB VAL A 125 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2506 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 64 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C ASN L 64 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN L 64 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL L 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 64 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASN H 64 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN H 64 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL H 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 80 " -0.007 2.00e-02 2.50e+03 1.33e-02 4.00e+00 pdb=" N1 DC O 80 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DC O 80 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DC O 80 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DC O 80 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC O 80 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC O 80 " -0.006 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 419 2.66 - 3.22: 13370 3.22 - 3.78: 29040 3.78 - 4.34: 34913 4.34 - 4.90: 49905 Nonbonded interactions: 127647 Sorted by model distance: nonbonded pdb=" N2 DG O 83 " pdb=" O2 DC P 65 " model vdw 2.098 2.496 nonbonded pdb=" OG1 THR A 217 " pdb=" OD1 ASP A 219 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLU L 52 " pdb=" N GLU L 53 " model vdw 2.219 3.120 nonbonded pdb=" OE1 GLU H 52 " pdb=" N GLU H 53 " model vdw 2.220 3.120 nonbonded pdb=" OP1 DA P 102 " pdb=" N LYS L 79 " model vdw 2.236 3.120 ... (remaining 127642 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 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.003 0.048 15271 Z= 0.159 Angle : 0.591 8.229 21915 Z= 0.368 Chirality : 0.036 0.141 2509 Planarity : 0.003 0.038 1765 Dihedral : 27.209 132.729 6396 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.58 % Allowed : 3.80 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1056 helix: -0.03 (0.20), residues: 546 sheet: -2.08 (0.44), residues: 134 loop : -2.45 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 36 TYR 0.008 0.001 TYR I 57 PHE 0.006 0.001 PHE H 100 TRP 0.016 0.001 TRP A 279 HIS 0.003 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00324 (15271) covalent geometry : angle 0.59145 (21915) hydrogen bonds : bond 0.11259 ( 856) hydrogen bonds : angle 5.12876 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 427 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8503 (m-80) cc_final: 0.8184 (m-80) REVERT: A 81 LEU cc_start: 0.8838 (mt) cc_final: 0.8471 (pp) REVERT: A 134 MET cc_start: 0.8204 (ttp) cc_final: 0.6762 (mpp) REVERT: A 251 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8545 (mmt180) REVERT: A 264 GLU cc_start: 0.7380 (tp30) cc_final: 0.7126 (tp30) REVERT: A 265 TYR cc_start: 0.7885 (m-10) cc_final: 0.7667 (m-10) REVERT: G 41 TYR cc_start: 0.8597 (m-80) cc_final: 0.8206 (m-80) REVERT: G 77 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.8920 (t70) REVERT: G 93 GLN cc_start: 0.9191 (tt0) cc_final: 0.8737 (tt0) REVERT: G 106 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8763 (p0) REVERT: G 107 THR cc_start: 0.9431 (p) cc_final: 0.8883 (p) REVERT: G 123 ASP cc_start: 0.8536 (t70) cc_final: 0.6799 (t70) REVERT: G 124 ILE cc_start: 0.9596 (mt) cc_final: 0.9289 (tp) REVERT: G 125 GLN cc_start: 0.9126 (mt0) cc_final: 0.8765 (mt0) REVERT: H 22 LEU cc_start: 0.7817 (mm) cc_final: 0.7129 (mm) REVERT: H 39 ARG cc_start: 0.9191 (mmt-90) cc_final: 0.8839 (tpp-160) REVERT: H 43 VAL cc_start: 0.8535 (t) cc_final: 0.7839 (t) REVERT: H 51 TYR cc_start: 0.8158 (m-80) cc_final: 0.6960 (m-10) REVERT: H 55 ARG cc_start: 0.9131 (mtt90) cc_final: 0.8757 (mtm-85) REVERT: H 64 ASN cc_start: 0.9109 (m-40) cc_final: 0.8687 (m-40) REVERT: H 75 HIS cc_start: 0.8678 (t70) cc_final: 0.8351 (t-90) REVERT: H 77 LYS cc_start: 0.9483 (mttt) cc_final: 0.9191 (mmtm) REVERT: I 17 ARG cc_start: 0.9387 (ttm110) cc_final: 0.9150 (ptp-110) REVERT: I 42 ARG cc_start: 0.9350 (mtm180) cc_final: 0.8920 (ttm110) REVERT: I 61 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8816 (tp30) REVERT: I 75 LYS cc_start: 0.9360 (mmtm) cc_final: 0.8984 (mmtp) REVERT: I 76 THR cc_start: 0.9233 (m) cc_final: 0.8920 (p) REVERT: I 84 GLN cc_start: 0.9603 (tp40) cc_final: 0.9402 (tp40) REVERT: I 94 ASN cc_start: 0.9066 (t0) cc_final: 0.8526 (t0) REVERT: I 95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9298 (tppt) REVERT: I 104 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8582 (mp10) REVERT: J 32 GLU cc_start: 0.9040 (pp20) cc_final: 0.8318 (pp20) REVERT: J 40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9330 (mtpt) REVERT: J 62 PHE cc_start: 0.9567 (t80) cc_final: 0.9157 (t80) REVERT: J 65 ASP cc_start: 0.8605 (t70) cc_final: 0.7658 (t0) REVERT: J 68 GLU cc_start: 0.9083 (tp30) cc_final: 0.8730 (tp30) REVERT: J 76 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8763 (ttm110) REVERT: J 81 ASN cc_start: 0.9278 (m-40) cc_final: 0.8402 (m-40) REVERT: J 85 THR cc_start: 0.8640 (p) cc_final: 0.8385 (p) REVERT: J 90 GLU cc_start: 0.9256 (mp0) cc_final: 0.9042 (mp0) REVERT: J 93 THR cc_start: 0.9750 (m) cc_final: 0.9500 (p) REVERT: J 102 GLU cc_start: 0.8794 (tp30) cc_final: 0.8572 (tm-30) REVERT: J 103 LEU cc_start: 0.9338 (mt) cc_final: 0.9035 (mt) REVERT: J 110 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9003 (mm-30) REVERT: K 48 LEU cc_start: 0.9613 (mp) cc_final: 0.9273 (mp) REVERT: K 50 GLU cc_start: 0.8350 (tp30) cc_final: 0.7676 (tp30) REVERT: K 52 ARG cc_start: 0.9252 (mtt90) cc_final: 0.8808 (mtm-85) REVERT: K 54 TYR cc_start: 0.8942 (m-10) cc_final: 0.8680 (m-10) REVERT: K 60 LEU cc_start: 0.9241 (mt) cc_final: 0.8952 (mt) REVERT: K 65 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9259 (tp) REVERT: K 67 PHE cc_start: 0.9575 (t80) cc_final: 0.9359 (t80) REVERT: K 68 GLN cc_start: 0.9305 (tt0) cc_final: 0.9006 (tt0) REVERT: K 86 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8298 (t) REVERT: K 93 GLN cc_start: 0.9622 (tt0) cc_final: 0.9395 (tm-30) REVERT: K 94 GLU cc_start: 0.9367 (tt0) cc_final: 0.9159 (tm-30) REVERT: K 110 CYS cc_start: 0.9470 (m) cc_final: 0.9265 (p) REVERT: K 121 PRO cc_start: 0.9110 (Cg_exo) cc_final: 0.8734 (Cg_endo) REVERT: K 123 ASP cc_start: 0.7897 (t70) cc_final: 0.6293 (t70) REVERT: K 124 ILE cc_start: 0.9656 (mt) cc_final: 0.9345 (mm) REVERT: M 36 LYS cc_start: 0.9139 (mttm) cc_final: 0.8822 (tttt) REVERT: M 42 ARG cc_start: 0.9210 (ptm160) cc_final: 0.8748 (ptm160) REVERT: M 64 GLU cc_start: 0.9463 (tt0) cc_final: 0.8913 (tm-30) REVERT: M 68 ASN cc_start: 0.9462 (m-40) cc_final: 0.8186 (m-40) REVERT: M 78 ILE cc_start: 0.9640 (mt) cc_final: 0.9402 (mm) REVERT: M 112 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8628 (mp10) REVERT: N 65 ASP cc_start: 0.9313 (t0) cc_final: 0.8890 (t0) REVERT: N 91 ILE cc_start: 0.9716 (mm) cc_final: 0.9317 (tt) REVERT: N 96 ARG cc_start: 0.9129 (mtp180) cc_final: 0.8601 (ttm110) REVERT: N 105 LYS cc_start: 0.9155 (mttt) cc_final: 0.8456 (mtpp) REVERT: N 110 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8409 (mt-10) REVERT: L 25 ASN cc_start: 0.8035 (t0) cc_final: 0.6530 (t0) REVERT: L 51 TYR cc_start: 0.8022 (m-80) cc_final: 0.7626 (m-80) REVERT: L 68 ASP cc_start: 0.9510 (m-30) cc_final: 0.9182 (m-30) REVERT: L 79 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7925 (mmmt) REVERT: L 82 THR cc_start: 0.9304 (p) cc_final: 0.9053 (p) REVERT: L 98 TYR cc_start: 0.8930 (m-10) cc_final: 0.8032 (m-80) outliers start: 32 outliers final: 11 residues processed: 436 average time/residue: 0.1471 time to fit residues: 87.5122 Evaluate side-chains 355 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 340 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 197 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 68 GLN H 25 ASN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN K 76 GLN K 108 ASN N 46 HIS L 25 ASN L 64 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.040816 restraints weight = 78925.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.042300 restraints weight = 36745.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.043263 restraints weight = 22618.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043830 restraints weight = 16533.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044220 restraints weight = 13666.629| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15271 Z= 0.249 Angle : 0.644 8.305 21915 Z= 0.370 Chirality : 0.039 0.195 2509 Planarity : 0.005 0.049 1765 Dihedral : 30.375 131.942 4372 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1056 helix: 1.18 (0.21), residues: 540 sheet: -2.02 (0.44), residues: 139 loop : -1.80 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 23 TYR 0.028 0.002 TYR H 88 PHE 0.029 0.002 PHE G 67 TRP 0.026 0.002 TRP A 35 HIS 0.007 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00539 (15271) covalent geometry : angle 0.64398 (21915) hydrogen bonds : bond 0.06221 ( 856) hydrogen bonds : angle 4.09877 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8438 (mtp) cc_final: 0.8047 (mtp) REVERT: A 81 LEU cc_start: 0.8815 (mt) cc_final: 0.8447 (pp) REVERT: A 134 MET cc_start: 0.7885 (ttp) cc_final: 0.6480 (mpp) REVERT: A 251 ARG cc_start: 0.9083 (mmt90) cc_final: 0.8634 (mmt180) REVERT: A 265 TYR cc_start: 0.7749 (m-10) cc_final: 0.7512 (m-10) REVERT: A 280 GLU cc_start: 0.8448 (tt0) cc_final: 0.8162 (tt0) REVERT: G 41 TYR cc_start: 0.8805 (m-80) cc_final: 0.8306 (m-80) REVERT: G 50 GLU cc_start: 0.8427 (tp30) cc_final: 0.8195 (tp30) REVERT: G 51 ILE cc_start: 0.9580 (mt) cc_final: 0.9327 (mm) REVERT: G 55 GLN cc_start: 0.9419 (mt0) cc_final: 0.9189 (mt0) REVERT: G 60 LEU cc_start: 0.9319 (mp) cc_final: 0.8978 (mp) REVERT: G 73 GLU cc_start: 0.8872 (tt0) cc_final: 0.8335 (tt0) REVERT: G 77 ASP cc_start: 0.9028 (t70) cc_final: 0.8700 (t70) REVERT: G 93 GLN cc_start: 0.9512 (tt0) cc_final: 0.9248 (tt0) REVERT: G 113 HIS cc_start: 0.9065 (t-170) cc_final: 0.8763 (t-170) REVERT: G 125 GLN cc_start: 0.9099 (mt0) cc_final: 0.8671 (mt0) REVERT: H 30 THR cc_start: 0.9328 (p) cc_final: 0.8929 (t) REVERT: H 44 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8649 (ttmt) REVERT: H 74 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8696 (tm-30) REVERT: H 77 LYS cc_start: 0.9445 (mttt) cc_final: 0.9242 (mttp) REVERT: I 61 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8952 (mm-30) REVERT: I 68 ASN cc_start: 0.9405 (m-40) cc_final: 0.9187 (m110) REVERT: I 75 LYS cc_start: 0.9524 (mmtm) cc_final: 0.9056 (mmtp) REVERT: I 76 THR cc_start: 0.9236 (m) cc_final: 0.8940 (p) REVERT: I 84 GLN cc_start: 0.9646 (tp40) cc_final: 0.9408 (tp40) REVERT: I 87 VAL cc_start: 0.9698 (m) cc_final: 0.9488 (m) REVERT: I 94 ASN cc_start: 0.9122 (t0) cc_final: 0.8606 (t0) REVERT: I 95 LYS cc_start: 0.9588 (tptt) cc_final: 0.9341 (tppt) REVERT: J 32 GLU cc_start: 0.9237 (pp20) cc_final: 0.8550 (pp20) REVERT: J 44 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8699 (tm-30) REVERT: J 65 ASP cc_start: 0.8472 (t70) cc_final: 0.7882 (t0) REVERT: J 68 GLU cc_start: 0.8935 (tp30) cc_final: 0.8694 (tp30) REVERT: J 73 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8771 (mm-30) REVERT: J 76 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8850 (ttm110) REVERT: J 77 LEU cc_start: 0.9657 (tp) cc_final: 0.9447 (tp) REVERT: J 81 ASN cc_start: 0.9240 (m-40) cc_final: 0.8159 (p0) REVERT: J 93 THR cc_start: 0.9751 (m) cc_final: 0.9507 (p) REVERT: J 98 LEU cc_start: 0.9194 (tt) cc_final: 0.8855 (tt) REVERT: K 41 TYR cc_start: 0.8909 (m-80) cc_final: 0.8689 (m-80) REVERT: K 50 GLU cc_start: 0.8249 (tp30) cc_final: 0.7779 (tp30) REVERT: K 85 GLN cc_start: 0.9429 (mm110) cc_final: 0.9185 (mm110) REVERT: K 90 MET cc_start: 0.8864 (ptp) cc_final: 0.8657 (ptp) REVERT: K 93 GLN cc_start: 0.9515 (tt0) cc_final: 0.9304 (tm-30) REVERT: K 120 MET cc_start: 0.9078 (mmp) cc_final: 0.8675 (mmm) REVERT: M 36 LYS cc_start: 0.9144 (mttm) cc_final: 0.8925 (pttt) REVERT: M 56 GLU cc_start: 0.9434 (tt0) cc_final: 0.9144 (mt-10) REVERT: M 57 TYR cc_start: 0.9381 (t80) cc_final: 0.9052 (t80) REVERT: M 64 GLU cc_start: 0.9477 (tt0) cc_final: 0.8976 (tm-30) REVERT: M 68 ASN cc_start: 0.9544 (m-40) cc_final: 0.8099 (m-40) REVERT: M 93 LEU cc_start: 0.9714 (tp) cc_final: 0.9440 (tt) REVERT: N 44 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9013 (tm-30) REVERT: N 56 MET cc_start: 0.9126 (tpt) cc_final: 0.8906 (tpp) REVERT: N 65 ASP cc_start: 0.9265 (t0) cc_final: 0.8842 (t0) REVERT: N 83 ARG cc_start: 0.8701 (mmt90) cc_final: 0.8352 (mmm160) REVERT: N 85 THR cc_start: 0.8862 (p) cc_final: 0.8008 (p) REVERT: N 96 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8573 (ttm110) REVERT: N 110 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8597 (mt-10) REVERT: L 25 ASN cc_start: 0.7527 (t0) cc_final: 0.6980 (t0) REVERT: L 51 TYR cc_start: 0.8673 (m-80) cc_final: 0.8273 (m-80) REVERT: L 54 THR cc_start: 0.9648 (m) cc_final: 0.9418 (p) REVERT: L 75 HIS cc_start: 0.8991 (t-90) cc_final: 0.8734 (t-90) REVERT: L 79 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8427 (mmtt) REVERT: L 88 TYR cc_start: 0.9306 (m-10) cc_final: 0.8474 (m-10) REVERT: L 98 TYR cc_start: 0.8841 (m-10) cc_final: 0.8615 (m-80) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1222 time to fit residues: 64.6776 Evaluate side-chains 312 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 126 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.042211 restraints weight = 77935.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043765 restraints weight = 35961.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.044791 restraints weight = 21912.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045417 restraints weight = 15844.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045776 restraints weight = 12948.731| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.173 Angle : 0.602 7.328 21915 Z= 0.349 Chirality : 0.038 0.193 2509 Planarity : 0.004 0.054 1765 Dihedral : 30.226 133.530 4372 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1056 helix: 1.61 (0.21), residues: 540 sheet: -1.83 (0.42), residues: 149 loop : -1.72 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 92 TYR 0.038 0.002 TYR H 88 PHE 0.033 0.002 PHE K 67 TRP 0.021 0.002 TRP A 279 HIS 0.008 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (15271) covalent geometry : angle 0.60175 (21915) hydrogen bonds : bond 0.05496 ( 856) hydrogen bonds : angle 3.77592 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8414 (mtp) cc_final: 0.8182 (mmp) REVERT: A 81 LEU cc_start: 0.8852 (mt) cc_final: 0.8565 (pp) REVERT: A 134 MET cc_start: 0.7852 (ttp) cc_final: 0.6636 (mpp) REVERT: A 251 ARG cc_start: 0.8963 (mmt90) cc_final: 0.8509 (mmt180) REVERT: A 259 PHE cc_start: 0.6685 (m-80) cc_final: 0.5777 (m-80) REVERT: A 265 TYR cc_start: 0.7644 (m-10) cc_final: 0.7383 (m-80) REVERT: A 280 GLU cc_start: 0.8598 (tt0) cc_final: 0.7992 (tt0) REVERT: G 41 TYR cc_start: 0.8714 (m-80) cc_final: 0.8159 (m-80) REVERT: G 50 GLU cc_start: 0.8311 (tp30) cc_final: 0.8082 (tp30) REVERT: G 55 GLN cc_start: 0.9449 (mt0) cc_final: 0.9206 (mt0) REVERT: G 60 LEU cc_start: 0.9334 (mp) cc_final: 0.8605 (mp) REVERT: G 63 ARG cc_start: 0.8231 (mmt-90) cc_final: 0.7756 (mmm-85) REVERT: G 77 ASP cc_start: 0.9106 (t70) cc_final: 0.8756 (t70) REVERT: G 93 GLN cc_start: 0.9496 (tt0) cc_final: 0.9185 (tm-30) REVERT: G 113 HIS cc_start: 0.9059 (t-170) cc_final: 0.8224 (t-170) REVERT: G 122 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8134 (ptpt) REVERT: G 125 GLN cc_start: 0.9117 (mt0) cc_final: 0.8643 (mp10) REVERT: H 30 THR cc_start: 0.9341 (p) cc_final: 0.8869 (t) REVERT: H 39 ARG cc_start: 0.9216 (mmt-90) cc_final: 0.8994 (mmp80) REVERT: H 43 VAL cc_start: 0.9557 (t) cc_final: 0.9106 (p) REVERT: H 45 ARG cc_start: 0.8840 (ttt-90) cc_final: 0.8602 (ttt-90) REVERT: H 68 ASP cc_start: 0.9133 (m-30) cc_final: 0.8746 (m-30) REVERT: H 74 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8734 (tm-30) REVERT: H 75 HIS cc_start: 0.8790 (t70) cc_final: 0.8572 (t-90) REVERT: H 77 LYS cc_start: 0.9498 (mttt) cc_final: 0.9295 (mmtp) REVERT: I 42 ARG cc_start: 0.9214 (mtm180) cc_final: 0.8950 (ttm110) REVERT: I 61 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8905 (mm-30) REVERT: I 73 ASN cc_start: 0.9232 (t0) cc_final: 0.8968 (t0) REVERT: I 75 LYS cc_start: 0.9520 (mmtm) cc_final: 0.9048 (mmtp) REVERT: I 76 THR cc_start: 0.9208 (m) cc_final: 0.8858 (p) REVERT: I 84 GLN cc_start: 0.9627 (tp40) cc_final: 0.9340 (tp40) REVERT: I 87 VAL cc_start: 0.9663 (m) cc_final: 0.9430 (m) REVERT: I 94 ASN cc_start: 0.9058 (t0) cc_final: 0.8579 (t0) REVERT: I 95 LYS cc_start: 0.9584 (tptt) cc_final: 0.9294 (tppt) REVERT: J 32 GLU cc_start: 0.9219 (pp20) cc_final: 0.8966 (pp20) REVERT: J 44 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8742 (tm-30) REVERT: J 65 ASP cc_start: 0.8518 (t70) cc_final: 0.7945 (t0) REVERT: J 73 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8664 (mm-30) REVERT: J 76 ARG cc_start: 0.9186 (ttm110) cc_final: 0.8913 (ttm110) REVERT: J 81 ASN cc_start: 0.9202 (m-40) cc_final: 0.8146 (p0) REVERT: J 87 THR cc_start: 0.9119 (p) cc_final: 0.8554 (p) REVERT: J 93 THR cc_start: 0.9742 (m) cc_final: 0.9518 (p) REVERT: J 98 LEU cc_start: 0.9211 (tt) cc_final: 0.8993 (tt) REVERT: J 99 LEU cc_start: 0.9433 (mt) cc_final: 0.9189 (mp) REVERT: K 50 GLU cc_start: 0.8523 (tp30) cc_final: 0.7652 (tp30) REVERT: K 52 ARG cc_start: 0.9239 (mtt90) cc_final: 0.8759 (mtm-85) REVERT: K 64 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8913 (mtmm) REVERT: K 65 LEU cc_start: 0.9630 (mm) cc_final: 0.9217 (mp) REVERT: K 68 GLN cc_start: 0.9313 (tt0) cc_final: 0.8958 (pp30) REVERT: K 97 GLU cc_start: 0.9066 (tt0) cc_final: 0.8607 (tt0) REVERT: K 110 CYS cc_start: 0.9235 (m) cc_final: 0.9007 (t) REVERT: K 120 MET cc_start: 0.9255 (mmp) cc_final: 0.8891 (mmm) REVERT: K 123 ASP cc_start: 0.7954 (t0) cc_final: 0.7208 (t70) REVERT: K 125 GLN cc_start: 0.9029 (mp-120) cc_final: 0.8797 (mm-40) REVERT: M 35 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: M 36 LYS cc_start: 0.9146 (mttm) cc_final: 0.8864 (pttt) REVERT: M 57 TYR cc_start: 0.9399 (t80) cc_final: 0.9081 (t80) REVERT: M 64 GLU cc_start: 0.9439 (tt0) cc_final: 0.8991 (tm-30) REVERT: M 68 ASN cc_start: 0.9550 (m-40) cc_final: 0.8160 (m-40) REVERT: N 42 LEU cc_start: 0.9579 (tp) cc_final: 0.9363 (tp) REVERT: N 44 GLN cc_start: 0.9320 (tm-30) cc_final: 0.9021 (tm-30) REVERT: N 51 ILE cc_start: 0.8534 (pt) cc_final: 0.8156 (pt) REVERT: N 65 ASP cc_start: 0.9216 (t0) cc_final: 0.8764 (t0) REVERT: N 76 ARG cc_start: 0.9320 (ttm-80) cc_final: 0.9038 (ttm-80) REVERT: N 80 TYR cc_start: 0.8686 (m-10) cc_final: 0.8421 (m-10) REVERT: N 83 ARG cc_start: 0.8702 (mmt90) cc_final: 0.8336 (mmm-85) REVERT: N 96 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8481 (ttm110) REVERT: N 105 LYS cc_start: 0.9334 (mttt) cc_final: 0.8865 (mtpt) REVERT: N 110 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8585 (mt-10) REVERT: L 25 ASN cc_start: 0.7778 (t0) cc_final: 0.7231 (t0) REVERT: L 39 ARG cc_start: 0.8937 (mmt-90) cc_final: 0.8589 (tpp-160) REVERT: L 44 LYS cc_start: 0.9411 (mtpt) cc_final: 0.8926 (mttt) REVERT: L 51 TYR cc_start: 0.8681 (m-80) cc_final: 0.8331 (m-80) REVERT: L 79 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8079 (mmtm) REVERT: L 88 TYR cc_start: 0.9177 (m-10) cc_final: 0.8425 (m-10) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.1376 time to fit residues: 71.6896 Evaluate side-chains 313 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 108 ASN K 125 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.040601 restraints weight = 79556.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.042068 restraints weight = 37088.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.043039 restraints weight = 22836.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043595 restraints weight = 16693.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044046 restraints weight = 13816.676| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15271 Z= 0.254 Angle : 0.640 7.200 21915 Z= 0.371 Chirality : 0.038 0.167 2509 Planarity : 0.005 0.058 1765 Dihedral : 30.153 133.264 4372 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1056 helix: 1.51 (0.21), residues: 542 sheet: -1.82 (0.43), residues: 149 loop : -1.75 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 89 TYR 0.047 0.003 TYR H 88 PHE 0.021 0.002 PHE G 67 TRP 0.024 0.002 TRP A 51 HIS 0.009 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00561 (15271) covalent geometry : angle 0.63955 (21915) hydrogen bonds : bond 0.06236 ( 856) hydrogen bonds : angle 3.96368 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8407 (mtp) cc_final: 0.8110 (mtp) REVERT: A 81 LEU cc_start: 0.8855 (mt) cc_final: 0.8491 (pp) REVERT: A 134 MET cc_start: 0.7846 (ttp) cc_final: 0.6710 (mpp) REVERT: A 251 ARG cc_start: 0.9053 (mmt90) cc_final: 0.8608 (mmt180) REVERT: A 265 TYR cc_start: 0.7604 (m-80) cc_final: 0.7340 (m-80) REVERT: A 280 GLU cc_start: 0.8705 (tt0) cc_final: 0.8211 (tt0) REVERT: G 50 GLU cc_start: 0.8396 (tp30) cc_final: 0.8168 (tp30) REVERT: G 51 ILE cc_start: 0.9603 (mt) cc_final: 0.9328 (mm) REVERT: G 55 GLN cc_start: 0.9419 (mt0) cc_final: 0.9143 (mt0) REVERT: G 63 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7540 (mmm-85) REVERT: G 77 ASP cc_start: 0.9184 (t70) cc_final: 0.8917 (t70) REVERT: G 80 THR cc_start: 0.8624 (p) cc_final: 0.8397 (p) REVERT: G 113 HIS cc_start: 0.9133 (t-170) cc_final: 0.8489 (t-170) REVERT: G 125 GLN cc_start: 0.9174 (mt0) cc_final: 0.8718 (mp10) REVERT: H 30 THR cc_start: 0.9439 (p) cc_final: 0.8940 (t) REVERT: H 43 VAL cc_start: 0.9630 (t) cc_final: 0.9379 (m) REVERT: H 44 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8695 (ttmm) REVERT: H 68 ASP cc_start: 0.9185 (m-30) cc_final: 0.8710 (m-30) REVERT: H 74 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8666 (tm-30) REVERT: H 75 HIS cc_start: 0.8964 (t70) cc_final: 0.8516 (t70) REVERT: H 77 LYS cc_start: 0.9524 (mttt) cc_final: 0.9241 (mmtt) REVERT: I 61 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8932 (mm-30) REVERT: I 75 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9153 (mmtp) REVERT: I 76 THR cc_start: 0.8998 (m) cc_final: 0.8738 (p) REVERT: I 87 VAL cc_start: 0.9672 (m) cc_final: 0.9435 (m) REVERT: I 94 ASN cc_start: 0.9077 (t0) cc_final: 0.8500 (t0) REVERT: I 95 LYS cc_start: 0.9611 (tptt) cc_final: 0.9295 (tppt) REVERT: I 104 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8732 (mp10) REVERT: J 32 GLU cc_start: 0.9244 (pp20) cc_final: 0.8980 (pp20) REVERT: J 44 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8760 (tm-30) REVERT: J 65 ASP cc_start: 0.8672 (t70) cc_final: 0.8363 (t0) REVERT: J 76 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8739 (ttm110) REVERT: J 81 ASN cc_start: 0.9118 (m-40) cc_final: 0.8117 (p0) REVERT: J 93 THR cc_start: 0.9791 (m) cc_final: 0.9477 (p) REVERT: J 99 LEU cc_start: 0.9483 (mt) cc_final: 0.9266 (mp) REVERT: K 41 TYR cc_start: 0.8884 (m-80) cc_final: 0.8547 (m-80) REVERT: K 50 GLU cc_start: 0.8555 (tp30) cc_final: 0.7883 (tp30) REVERT: K 52 ARG cc_start: 0.9255 (mtt90) cc_final: 0.8875 (mtm-85) REVERT: K 68 GLN cc_start: 0.9318 (tt0) cc_final: 0.8994 (pp30) REVERT: K 84 PHE cc_start: 0.9151 (m-80) cc_final: 0.8694 (m-10) REVERT: K 97 GLU cc_start: 0.9031 (tt0) cc_final: 0.8775 (tt0) REVERT: K 106 ASP cc_start: 0.8936 (m-30) cc_final: 0.8725 (m-30) REVERT: K 110 CYS cc_start: 0.9330 (m) cc_final: 0.9006 (t) REVERT: K 120 MET cc_start: 0.9350 (mmp) cc_final: 0.8936 (mmm) REVERT: K 123 ASP cc_start: 0.8239 (t0) cc_final: 0.6569 (t0) REVERT: K 125 GLN cc_start: 0.8908 (mp10) cc_final: 0.8687 (mm-40) REVERT: M 36 LYS cc_start: 0.9112 (mttm) cc_final: 0.8873 (pttt) REVERT: M 57 TYR cc_start: 0.9538 (t80) cc_final: 0.9112 (t80) REVERT: M 64 GLU cc_start: 0.9470 (tt0) cc_final: 0.8993 (tm-30) REVERT: M 68 ASN cc_start: 0.9527 (m-40) cc_final: 0.8082 (m-40) REVERT: N 34 TYR cc_start: 0.9603 (m-80) cc_final: 0.9349 (m-10) REVERT: N 44 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9002 (tm-30) REVERT: N 58 ILE cc_start: 0.9651 (mt) cc_final: 0.9450 (mm) REVERT: N 65 ASP cc_start: 0.9255 (t0) cc_final: 0.8901 (t0) REVERT: N 83 ARG cc_start: 0.8759 (mmt90) cc_final: 0.8421 (mmm-85) REVERT: N 96 ARG cc_start: 0.8919 (mtp180) cc_final: 0.8545 (ttm110) REVERT: N 105 LYS cc_start: 0.9266 (mttt) cc_final: 0.8477 (mtpp) REVERT: N 110 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8604 (mt-10) REVERT: L 25 ASN cc_start: 0.7734 (t0) cc_final: 0.7226 (t0) REVERT: L 39 ARG cc_start: 0.9013 (mmt-90) cc_final: 0.8472 (tpp-160) REVERT: L 44 LYS cc_start: 0.9397 (mtpt) cc_final: 0.8658 (mttt) REVERT: L 63 GLU cc_start: 0.8792 (tp30) cc_final: 0.8523 (tp30) REVERT: L 68 ASP cc_start: 0.9184 (m-30) cc_final: 0.8793 (m-30) REVERT: L 79 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8141 (mmtm) REVERT: L 92 ARG cc_start: 0.8418 (tmm-80) cc_final: 0.7085 (ttp-170) REVERT: L 98 TYR cc_start: 0.8961 (m-80) cc_final: 0.8755 (m-80) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1278 time to fit residues: 62.8596 Evaluate side-chains 291 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN G 113 HIS H 75 HIS J 81 ASN K 93 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042914 restraints weight = 76768.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044434 restraints weight = 35774.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045463 restraints weight = 22024.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.046072 restraints weight = 15947.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046467 restraints weight = 13066.307| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.165 Angle : 0.608 6.971 21915 Z= 0.353 Chirality : 0.038 0.160 2509 Planarity : 0.004 0.058 1765 Dihedral : 30.064 133.857 4372 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1056 helix: 1.65 (0.21), residues: 542 sheet: -1.64 (0.42), residues: 155 loop : -1.65 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 77 TYR 0.055 0.003 TYR H 88 PHE 0.017 0.001 PHE J 62 TRP 0.022 0.002 TRP A 279 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (15271) covalent geometry : angle 0.60766 (21915) hydrogen bonds : bond 0.05367 ( 856) hydrogen bonds : angle 3.70140 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8331 (mtp) cc_final: 0.8120 (mmp) REVERT: A 81 LEU cc_start: 0.8806 (mt) cc_final: 0.8445 (pp) REVERT: A 134 MET cc_start: 0.7705 (ttp) cc_final: 0.6779 (mpp) REVERT: A 142 HIS cc_start: 0.8759 (p90) cc_final: 0.8555 (p90) REVERT: A 251 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8527 (mmt90) REVERT: A 259 PHE cc_start: 0.6742 (m-80) cc_final: 0.5960 (m-80) REVERT: A 265 TYR cc_start: 0.7374 (m-80) cc_final: 0.7079 (m-80) REVERT: A 280 GLU cc_start: 0.8645 (tt0) cc_final: 0.8076 (tt0) REVERT: G 41 TYR cc_start: 0.8773 (m-80) cc_final: 0.8509 (m-80) REVERT: G 55 GLN cc_start: 0.9461 (mt0) cc_final: 0.9230 (mt0) REVERT: G 63 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7521 (mmm-85) REVERT: G 67 PHE cc_start: 0.9437 (t80) cc_final: 0.9185 (t80) REVERT: G 77 ASP cc_start: 0.9236 (t70) cc_final: 0.8969 (t70) REVERT: G 113 HIS cc_start: 0.9070 (t70) cc_final: 0.8811 (t-170) REVERT: G 125 GLN cc_start: 0.9215 (mt0) cc_final: 0.8768 (mp10) REVERT: H 30 THR cc_start: 0.9470 (p) cc_final: 0.8987 (t) REVERT: H 71 THR cc_start: 0.9850 (m) cc_final: 0.9486 (p) REVERT: H 74 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8598 (tm-30) REVERT: H 85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8988 (m-30) REVERT: I 42 ARG cc_start: 0.9188 (mtm180) cc_final: 0.8678 (ttp-110) REVERT: I 57 TYR cc_start: 0.9325 (t80) cc_final: 0.8458 (t80) REVERT: I 61 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8599 (tp30) REVERT: I 75 LYS cc_start: 0.9599 (mmtm) cc_final: 0.9172 (mmtp) REVERT: I 87 VAL cc_start: 0.9654 (m) cc_final: 0.9383 (m) REVERT: I 90 ASP cc_start: 0.8999 (t0) cc_final: 0.8782 (t70) REVERT: I 94 ASN cc_start: 0.9023 (t0) cc_final: 0.8563 (t0) REVERT: I 95 LYS cc_start: 0.9581 (tptt) cc_final: 0.9290 (tppt) REVERT: I 104 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8711 (mp10) REVERT: J 32 GLU cc_start: 0.9259 (pp20) cc_final: 0.8988 (pp20) REVERT: J 43 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8871 (mmtm) REVERT: J 44 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8746 (tm-30) REVERT: J 65 ASP cc_start: 0.8540 (t70) cc_final: 0.8232 (t0) REVERT: J 81 ASN cc_start: 0.8821 (m110) cc_final: 0.8037 (p0) REVERT: J 85 THR cc_start: 0.8963 (p) cc_final: 0.7877 (p) REVERT: J 99 LEU cc_start: 0.9335 (mt) cc_final: 0.9060 (mp) REVERT: J 103 LEU cc_start: 0.9239 (mm) cc_final: 0.8598 (mm) REVERT: K 50 GLU cc_start: 0.8834 (tp30) cc_final: 0.7600 (tp30) REVERT: K 64 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8956 (mtmm) REVERT: K 68 GLN cc_start: 0.9267 (tt0) cc_final: 0.8980 (pp30) REVERT: K 73 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7139 (mt-10) REVERT: K 84 PHE cc_start: 0.9153 (m-80) cc_final: 0.8742 (m-10) REVERT: K 97 GLU cc_start: 0.8953 (tt0) cc_final: 0.8657 (tt0) REVERT: K 99 TYR cc_start: 0.9460 (t80) cc_final: 0.9153 (t80) REVERT: K 107 THR cc_start: 0.9154 (t) cc_final: 0.8574 (t) REVERT: K 120 MET cc_start: 0.9403 (mmp) cc_final: 0.9017 (mmm) REVERT: K 123 ASP cc_start: 0.8068 (t0) cc_final: 0.6548 (t0) REVERT: K 125 GLN cc_start: 0.9015 (mp10) cc_final: 0.8807 (mm-40) REVERT: M 36 LYS cc_start: 0.9077 (mttm) cc_final: 0.8826 (pttt) REVERT: M 57 TYR cc_start: 0.9522 (t80) cc_final: 0.9192 (t80) REVERT: M 64 GLU cc_start: 0.9442 (tt0) cc_final: 0.9001 (tm-30) REVERT: M 68 ASN cc_start: 0.9594 (m-40) cc_final: 0.8236 (m-40) REVERT: M 84 GLN cc_start: 0.9128 (tp40) cc_final: 0.8819 (tp40) REVERT: M 99 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7574 (tpt170) REVERT: M 102 ILE cc_start: 0.9604 (tp) cc_final: 0.9310 (tp) REVERT: N 44 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8997 (tm-30) REVERT: N 65 ASP cc_start: 0.9283 (t0) cc_final: 0.8884 (t0) REVERT: N 83 ARG cc_start: 0.8703 (mmt90) cc_final: 0.8384 (mmm-85) REVERT: N 96 ARG cc_start: 0.8830 (mtp180) cc_final: 0.8480 (ttm110) REVERT: N 110 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8541 (mt-10) REVERT: L 39 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8413 (tpp-160) REVERT: L 68 ASP cc_start: 0.9119 (m-30) cc_final: 0.8823 (m-30) REVERT: L 79 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7914 (mmtm) REVERT: L 92 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.7709 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1255 time to fit residues: 63.5986 Evaluate side-chains 307 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 75 optimal weight: 0.0050 chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 291 HIS G 68 GLN G 108 ASN G 113 HIS H 75 HIS K 93 GLN K 108 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043038 restraints weight = 77736.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044560 restraints weight = 36255.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045563 restraints weight = 22262.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046194 restraints weight = 16194.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046519 restraints weight = 13238.933| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15271 Z= 0.178 Angle : 0.609 7.885 21915 Z= 0.355 Chirality : 0.038 0.151 2509 Planarity : 0.004 0.059 1765 Dihedral : 29.955 134.438 4372 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1056 helix: 1.69 (0.21), residues: 540 sheet: -1.48 (0.44), residues: 150 loop : -1.61 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 76 TYR 0.061 0.003 TYR H 88 PHE 0.024 0.002 PHE K 67 TRP 0.027 0.002 TRP A 51 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (15271) covalent geometry : angle 0.60948 (21915) hydrogen bonds : bond 0.05450 ( 856) hydrogen bonds : angle 3.71499 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8948 (mt) cc_final: 0.8538 (pp) REVERT: A 134 MET cc_start: 0.7742 (ttp) cc_final: 0.6650 (mpp) REVERT: A 142 HIS cc_start: 0.8800 (p90) cc_final: 0.8520 (p90) REVERT: A 251 ARG cc_start: 0.8976 (mmt90) cc_final: 0.8555 (mmt90) REVERT: A 259 PHE cc_start: 0.6893 (m-80) cc_final: 0.6487 (m-80) REVERT: A 265 TYR cc_start: 0.7277 (m-80) cc_final: 0.7005 (m-80) REVERT: A 280 GLU cc_start: 0.8616 (tt0) cc_final: 0.8023 (tt0) REVERT: G 41 TYR cc_start: 0.8733 (m-80) cc_final: 0.8486 (m-80) REVERT: G 55 GLN cc_start: 0.9468 (mt0) cc_final: 0.9129 (mt0) REVERT: G 60 LEU cc_start: 0.9041 (mp) cc_final: 0.8782 (mt) REVERT: G 63 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.7495 (mmm-85) REVERT: G 77 ASP cc_start: 0.9238 (t70) cc_final: 0.8948 (t70) REVERT: G 93 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8611 (tm-30) REVERT: G 94 GLU cc_start: 0.9337 (tt0) cc_final: 0.9117 (tt0) REVERT: G 113 HIS cc_start: 0.8916 (t-170) cc_final: 0.8122 (t-170) REVERT: H 30 THR cc_start: 0.9408 (p) cc_final: 0.8801 (t) REVERT: H 31 LYS cc_start: 0.9242 (tmtt) cc_final: 0.9027 (tptp) REVERT: H 39 ARG cc_start: 0.9161 (mmt-90) cc_final: 0.8561 (mpp-170) REVERT: H 51 TYR cc_start: 0.8329 (m-10) cc_final: 0.7827 (m-10) REVERT: H 74 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8621 (tm-30) REVERT: H 75 HIS cc_start: 0.8737 (t-90) cc_final: 0.8455 (t70) REVERT: H 97 LEU cc_start: 0.9704 (tp) cc_final: 0.9442 (tp) REVERT: I 42 ARG cc_start: 0.9215 (mtm180) cc_final: 0.8685 (ttp-110) REVERT: I 57 TYR cc_start: 0.9315 (t80) cc_final: 0.8611 (t80) REVERT: I 61 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8617 (tp30) REVERT: I 73 ASN cc_start: 0.9228 (t0) cc_final: 0.8948 (t0) REVERT: I 75 LYS cc_start: 0.9524 (mmtm) cc_final: 0.9082 (mmtp) REVERT: I 87 VAL cc_start: 0.9648 (m) cc_final: 0.9330 (m) REVERT: I 90 ASP cc_start: 0.9127 (t0) cc_final: 0.8692 (t0) REVERT: I 94 ASN cc_start: 0.8940 (t0) cc_final: 0.8263 (m-40) REVERT: I 95 LYS cc_start: 0.9591 (tptt) cc_final: 0.9274 (tppt) REVERT: I 102 ILE cc_start: 0.9637 (mm) cc_final: 0.9379 (mt) REVERT: I 104 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8767 (mp10) REVERT: J 32 GLU cc_start: 0.9262 (pp20) cc_final: 0.9015 (pp20) REVERT: J 43 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8777 (mmtm) REVERT: J 44 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8724 (tm-30) REVERT: J 65 ASP cc_start: 0.8720 (t70) cc_final: 0.8206 (t0) REVERT: J 81 ASN cc_start: 0.8541 (m110) cc_final: 0.7752 (p0) REVERT: J 85 THR cc_start: 0.8983 (p) cc_final: 0.7867 (p) REVERT: J 97 LEU cc_start: 0.9468 (mt) cc_final: 0.9237 (mt) REVERT: J 98 LEU cc_start: 0.9156 (tt) cc_final: 0.8913 (tt) REVERT: J 99 LEU cc_start: 0.9299 (mt) cc_final: 0.9059 (mp) REVERT: K 50 GLU cc_start: 0.8891 (tp30) cc_final: 0.7764 (tp30) REVERT: K 65 LEU cc_start: 0.9637 (mm) cc_final: 0.8973 (mm) REVERT: K 68 GLN cc_start: 0.9244 (tt0) cc_final: 0.8922 (pp30) REVERT: K 84 PHE cc_start: 0.9125 (m-80) cc_final: 0.8734 (m-10) REVERT: K 93 GLN cc_start: 0.8784 (tm130) cc_final: 0.8575 (tm-30) REVERT: K 97 GLU cc_start: 0.8910 (tt0) cc_final: 0.8589 (mt-10) REVERT: K 110 CYS cc_start: 0.8708 (t) cc_final: 0.8479 (t) REVERT: K 120 MET cc_start: 0.9398 (mmp) cc_final: 0.8981 (mmm) REVERT: K 123 ASP cc_start: 0.7833 (t0) cc_final: 0.6929 (t70) REVERT: M 36 LYS cc_start: 0.9077 (mttm) cc_final: 0.8812 (pttt) REVERT: M 56 GLU cc_start: 0.9366 (tt0) cc_final: 0.9015 (mt-10) REVERT: M 64 GLU cc_start: 0.9446 (tt0) cc_final: 0.9002 (tm-30) REVERT: M 68 ASN cc_start: 0.9584 (m-40) cc_final: 0.8209 (m-40) REVERT: M 84 GLN cc_start: 0.9135 (tp40) cc_final: 0.8801 (tp40) REVERT: M 99 ARG cc_start: 0.7813 (tpt170) cc_final: 0.7565 (tpt170) REVERT: M 102 ILE cc_start: 0.9631 (tp) cc_final: 0.9351 (tp) REVERT: N 39 TYR cc_start: 0.7794 (t80) cc_final: 0.7528 (t80) REVERT: N 44 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9032 (tm-30) REVERT: N 58 ILE cc_start: 0.9486 (mt) cc_final: 0.9284 (mm) REVERT: N 65 ASP cc_start: 0.9255 (t0) cc_final: 0.8844 (t0) REVERT: N 68 GLU cc_start: 0.8436 (tp30) cc_final: 0.8209 (tp30) REVERT: N 83 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8186 (mmm160) REVERT: N 110 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8409 (tp30) REVERT: L 39 ARG cc_start: 0.8880 (mmt-90) cc_final: 0.8572 (tpp-160) REVERT: L 43 VAL cc_start: 0.9668 (m) cc_final: 0.9461 (m) REVERT: L 77 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9069 (mmtp) REVERT: L 79 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7764 (mmtm) REVERT: L 98 TYR cc_start: 0.8895 (m-80) cc_final: 0.8145 (m-80) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.1301 time to fit residues: 64.6456 Evaluate side-chains 299 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 91 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 328 ASN G 68 GLN G 76 GLN G 108 ASN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN K 125 GLN N 92 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.059419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044422 restraints weight = 76597.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045969 restraints weight = 36249.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047000 restraints weight = 22361.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047583 restraints weight = 16302.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048002 restraints weight = 13429.932| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15271 Z= 0.158 Angle : 0.612 8.276 21915 Z= 0.354 Chirality : 0.038 0.203 2509 Planarity : 0.004 0.060 1765 Dihedral : 29.867 134.386 4372 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.22 % Allowed : 2.24 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1056 helix: 1.70 (0.22), residues: 538 sheet: -1.18 (0.46), residues: 145 loop : -1.56 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 96 TYR 0.028 0.003 TYR N 80 PHE 0.023 0.002 PHE K 67 TRP 0.022 0.002 TRP A 279 HIS 0.006 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00349 (15271) covalent geometry : angle 0.61188 (21915) hydrogen bonds : bond 0.05248 ( 856) hydrogen bonds : angle 3.64822 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7681 (t60) cc_final: 0.7433 (t60) REVERT: A 81 LEU cc_start: 0.8957 (mt) cc_final: 0.8528 (pp) REVERT: A 134 MET cc_start: 0.7620 (ttp) cc_final: 0.6677 (mpp) REVERT: A 142 HIS cc_start: 0.8754 (p90) cc_final: 0.8460 (p90) REVERT: A 259 PHE cc_start: 0.6574 (m-80) cc_final: 0.5697 (m-80) REVERT: A 264 GLU cc_start: 0.7670 (tp30) cc_final: 0.7385 (tp30) REVERT: A 265 TYR cc_start: 0.7159 (m-80) cc_final: 0.6929 (m-80) REVERT: A 280 GLU cc_start: 0.8592 (tt0) cc_final: 0.8063 (tt0) REVERT: G 55 GLN cc_start: 0.9391 (mt0) cc_final: 0.9149 (mt0) REVERT: G 63 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7627 (mmm-85) REVERT: G 77 ASP cc_start: 0.9263 (t70) cc_final: 0.9022 (t70) REVERT: G 113 HIS cc_start: 0.8952 (t-170) cc_final: 0.8206 (t-170) REVERT: H 30 THR cc_start: 0.9298 (p) cc_final: 0.8727 (t) REVERT: H 51 TYR cc_start: 0.8183 (m-10) cc_final: 0.7894 (m-10) REVERT: H 71 THR cc_start: 0.9821 (m) cc_final: 0.9480 (p) REVERT: H 74 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8720 (tm-30) REVERT: I 42 ARG cc_start: 0.9190 (mtm180) cc_final: 0.8968 (ttp-110) REVERT: I 61 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8941 (mm-30) REVERT: I 71 ARG cc_start: 0.9026 (ttp-170) cc_final: 0.8790 (ttp80) REVERT: I 73 ASN cc_start: 0.9226 (t0) cc_final: 0.8934 (t0) REVERT: I 75 LYS cc_start: 0.9441 (mmtm) cc_final: 0.9064 (mmtp) REVERT: I 87 VAL cc_start: 0.9615 (m) cc_final: 0.9277 (m) REVERT: I 90 ASP cc_start: 0.9159 (t0) cc_final: 0.8657 (t0) REVERT: I 94 ASN cc_start: 0.8888 (t0) cc_final: 0.8190 (m-40) REVERT: I 95 LYS cc_start: 0.9532 (tptt) cc_final: 0.9216 (tppt) REVERT: I 115 LEU cc_start: 0.9340 (mm) cc_final: 0.9015 (mm) REVERT: J 43 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8714 (mmtm) REVERT: J 44 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8577 (tm-30) REVERT: J 65 ASP cc_start: 0.8730 (t70) cc_final: 0.8492 (t70) REVERT: J 76 ARG cc_start: 0.9272 (ttm110) cc_final: 0.8899 (ttm110) REVERT: J 81 ASN cc_start: 0.8545 (m110) cc_final: 0.7862 (p0) REVERT: J 85 THR cc_start: 0.9029 (p) cc_final: 0.8563 (p) REVERT: J 99 LEU cc_start: 0.9226 (mt) cc_final: 0.8986 (mp) REVERT: J 105 LYS cc_start: 0.9230 (mmtm) cc_final: 0.9025 (mmmm) REVERT: K 50 GLU cc_start: 0.8831 (tp30) cc_final: 0.7855 (tp30) REVERT: K 64 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8962 (mtmm) REVERT: K 65 LEU cc_start: 0.9608 (mm) cc_final: 0.9112 (mp) REVERT: K 68 GLN cc_start: 0.9212 (tt0) cc_final: 0.8922 (pp30) REVERT: K 84 PHE cc_start: 0.9141 (m-80) cc_final: 0.8780 (m-10) REVERT: K 97 GLU cc_start: 0.8977 (tt0) cc_final: 0.8638 (mt-10) REVERT: K 110 CYS cc_start: 0.8681 (t) cc_final: 0.8461 (t) REVERT: K 120 MET cc_start: 0.9462 (mmp) cc_final: 0.9123 (mmm) REVERT: K 123 ASP cc_start: 0.7771 (t0) cc_final: 0.6872 (t70) REVERT: M 36 LYS cc_start: 0.9065 (mttm) cc_final: 0.8785 (pttt) REVERT: M 56 GLU cc_start: 0.9353 (tt0) cc_final: 0.9022 (mt-10) REVERT: M 62 ILE cc_start: 0.9660 (mm) cc_final: 0.9266 (tt) REVERT: M 64 GLU cc_start: 0.9409 (tt0) cc_final: 0.8963 (tm-30) REVERT: M 68 ASN cc_start: 0.9586 (m-40) cc_final: 0.8272 (m-40) REVERT: M 99 ARG cc_start: 0.7907 (tpt170) cc_final: 0.7603 (tpt170) REVERT: M 102 ILE cc_start: 0.9630 (tp) cc_final: 0.9402 (tp) REVERT: N 44 GLN cc_start: 0.9296 (tm-30) cc_final: 0.9029 (tm-30) REVERT: N 58 ILE cc_start: 0.9461 (mt) cc_final: 0.9243 (mm) REVERT: N 65 ASP cc_start: 0.9231 (t0) cc_final: 0.8886 (t0) REVERT: N 80 TYR cc_start: 0.7829 (m-80) cc_final: 0.6964 (m-10) REVERT: N 83 ARG cc_start: 0.8570 (mmt90) cc_final: 0.8158 (mmm160) REVERT: N 105 LYS cc_start: 0.9258 (mttt) cc_final: 0.8771 (mtmt) REVERT: N 110 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8385 (tp30) REVERT: N 113 LYS cc_start: 0.9460 (tmmt) cc_final: 0.9223 (ttpp) REVERT: L 39 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.8494 (tpp-160) REVERT: L 44 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8691 (mttt) REVERT: L 68 ASP cc_start: 0.9126 (m-30) cc_final: 0.8736 (m-30) REVERT: L 77 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9065 (mmtp) REVERT: L 79 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7797 (mmtm) REVERT: L 98 TYR cc_start: 0.8878 (m-80) cc_final: 0.8651 (m-80) outliers start: 2 outliers final: 0 residues processed: 360 average time/residue: 0.1349 time to fit residues: 69.0848 Evaluate side-chains 306 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 108 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN K 125 GLN L 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044423 restraints weight = 76644.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045969 restraints weight = 36169.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046987 restraints weight = 22171.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047606 restraints weight = 16101.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047990 restraints weight = 13179.447| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15271 Z= 0.169 Angle : 0.615 6.964 21915 Z= 0.356 Chirality : 0.037 0.163 2509 Planarity : 0.005 0.083 1765 Dihedral : 29.816 134.664 4372 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.34 % Allowed : 1.68 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1056 helix: 1.65 (0.21), residues: 536 sheet: -1.14 (0.46), residues: 145 loop : -1.45 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 96 TYR 0.030 0.003 TYR L 88 PHE 0.020 0.002 PHE A 206 TRP 0.017 0.002 TRP A 279 HIS 0.011 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (15271) covalent geometry : angle 0.61462 (21915) hydrogen bonds : bond 0.05311 ( 856) hydrogen bonds : angle 3.69275 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7787 (t60) cc_final: 0.7488 (t60) REVERT: A 81 LEU cc_start: 0.8910 (mt) cc_final: 0.8483 (pp) REVERT: A 134 MET cc_start: 0.7583 (ttp) cc_final: 0.6541 (mpp) REVERT: A 167 TYR cc_start: 0.6966 (m-10) cc_final: 0.6737 (m-80) REVERT: A 225 TYR cc_start: 0.7518 (m-10) cc_final: 0.7190 (m-10) REVERT: A 264 GLU cc_start: 0.7695 (tp30) cc_final: 0.7435 (tp30) REVERT: A 280 GLU cc_start: 0.8650 (tt0) cc_final: 0.8157 (tt0) REVERT: G 60 LEU cc_start: 0.8967 (mp) cc_final: 0.8648 (mt) REVERT: G 63 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7628 (mmm-85) REVERT: G 73 GLU cc_start: 0.8769 (tt0) cc_final: 0.8345 (tt0) REVERT: G 77 ASP cc_start: 0.9286 (t70) cc_final: 0.9070 (t70) REVERT: G 113 HIS cc_start: 0.8960 (t-170) cc_final: 0.8130 (t-170) REVERT: G 125 GLN cc_start: 0.9135 (mt0) cc_final: 0.8674 (mp10) REVERT: H 30 THR cc_start: 0.9272 (p) cc_final: 0.8672 (t) REVERT: H 31 LYS cc_start: 0.9032 (tptp) cc_final: 0.8535 (tptp) REVERT: H 51 TYR cc_start: 0.8177 (m-10) cc_final: 0.7562 (m-10) REVERT: I 38 ASN cc_start: 0.8636 (m-40) cc_final: 0.8316 (m-40) REVERT: I 42 ARG cc_start: 0.9182 (mtm180) cc_final: 0.8957 (ttp-110) REVERT: I 71 ARG cc_start: 0.9062 (ttp-170) cc_final: 0.8830 (ttp80) REVERT: I 73 ASN cc_start: 0.9221 (t0) cc_final: 0.8920 (t0) REVERT: I 75 LYS cc_start: 0.9465 (mmtm) cc_final: 0.9036 (mmtp) REVERT: I 87 VAL cc_start: 0.9634 (m) cc_final: 0.9226 (m) REVERT: I 90 ASP cc_start: 0.9140 (t0) cc_final: 0.8637 (t0) REVERT: I 94 ASN cc_start: 0.8911 (t0) cc_final: 0.8252 (m-40) REVERT: I 95 LYS cc_start: 0.9524 (tptt) cc_final: 0.9285 (ttmm) REVERT: I 104 GLN cc_start: 0.8816 (mp10) cc_final: 0.8112 (mp10) REVERT: J 43 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8687 (mmtm) REVERT: J 44 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8608 (tm-30) REVERT: J 65 ASP cc_start: 0.8695 (t70) cc_final: 0.8237 (t0) REVERT: J 76 ARG cc_start: 0.9227 (ttm110) cc_final: 0.8804 (ttm110) REVERT: J 81 ASN cc_start: 0.8584 (m110) cc_final: 0.7924 (p0) REVERT: J 85 THR cc_start: 0.9046 (p) cc_final: 0.8565 (p) REVERT: J 99 LEU cc_start: 0.9285 (mt) cc_final: 0.9018 (mp) REVERT: K 50 GLU cc_start: 0.8841 (tp30) cc_final: 0.8112 (tp30) REVERT: K 54 TYR cc_start: 0.8335 (m-10) cc_final: 0.7983 (m-10) REVERT: K 64 LYS cc_start: 0.9258 (mtmt) cc_final: 0.9013 (mtmm) REVERT: K 84 PHE cc_start: 0.9151 (m-80) cc_final: 0.8804 (m-10) REVERT: K 86 SER cc_start: 0.8961 (p) cc_final: 0.7648 (t) REVERT: K 90 MET cc_start: 0.9011 (mtm) cc_final: 0.8479 (mtt) REVERT: K 93 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8456 (tm-30) REVERT: K 97 GLU cc_start: 0.8910 (tt0) cc_final: 0.8548 (mt-10) REVERT: K 110 CYS cc_start: 0.8780 (t) cc_final: 0.8521 (t) REVERT: K 120 MET cc_start: 0.9432 (mmp) cc_final: 0.9099 (mmm) REVERT: K 123 ASP cc_start: 0.7822 (t0) cc_final: 0.6867 (t70) REVERT: M 36 LYS cc_start: 0.9077 (mttm) cc_final: 0.8812 (pttt) REVERT: M 56 GLU cc_start: 0.9344 (tt0) cc_final: 0.9039 (mt-10) REVERT: M 62 ILE cc_start: 0.9703 (mm) cc_final: 0.9266 (tt) REVERT: M 64 GLU cc_start: 0.9431 (tt0) cc_final: 0.8964 (tm-30) REVERT: M 68 ASN cc_start: 0.9586 (m-40) cc_final: 0.8267 (m-40) REVERT: N 44 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9021 (tm-30) REVERT: N 58 ILE cc_start: 0.9489 (mt) cc_final: 0.9261 (mm) REVERT: N 65 ASP cc_start: 0.9237 (t0) cc_final: 0.8894 (t0) REVERT: N 76 ARG cc_start: 0.8867 (ttt90) cc_final: 0.8431 (ttt-90) REVERT: N 80 TYR cc_start: 0.7667 (m-80) cc_final: 0.7262 (m-10) REVERT: N 83 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8227 (mmm-85) REVERT: N 110 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8397 (tp30) REVERT: N 113 LYS cc_start: 0.9458 (tmmt) cc_final: 0.9173 (ttpp) REVERT: L 39 ARG cc_start: 0.8822 (mmt-90) cc_final: 0.8414 (tpp-160) REVERT: L 91 LYS cc_start: 0.9227 (tttm) cc_final: 0.9003 (ttpt) outliers start: 3 outliers final: 1 residues processed: 344 average time/residue: 0.1336 time to fit residues: 65.3303 Evaluate side-chains 302 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043926 restraints weight = 77869.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045463 restraints weight = 36870.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046475 restraints weight = 22783.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047081 restraints weight = 16601.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047434 restraints weight = 13623.809| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15271 Z= 0.186 Angle : 0.629 8.262 21915 Z= 0.361 Chirality : 0.038 0.159 2509 Planarity : 0.005 0.075 1765 Dihedral : 29.813 139.288 4372 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1056 helix: 1.72 (0.22), residues: 532 sheet: -1.11 (0.46), residues: 145 loop : -1.36 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 96 TYR 0.027 0.002 TYR L 88 PHE 0.020 0.002 PHE A 206 TRP 0.017 0.002 TRP A 74 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00415 (15271) covalent geometry : angle 0.62851 (21915) hydrogen bonds : bond 0.05396 ( 856) hydrogen bonds : angle 3.73480 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7715 (t60) cc_final: 0.7418 (t60) REVERT: A 81 LEU cc_start: 0.8878 (mt) cc_final: 0.8442 (pp) REVERT: A 134 MET cc_start: 0.7599 (ttp) cc_final: 0.6479 (mpp) REVERT: A 225 TYR cc_start: 0.7630 (m-10) cc_final: 0.7294 (m-10) REVERT: A 264 GLU cc_start: 0.7655 (tp30) cc_final: 0.7385 (tp30) REVERT: A 280 GLU cc_start: 0.8687 (tt0) cc_final: 0.8139 (tt0) REVERT: A 321 TRP cc_start: 0.6877 (m100) cc_final: 0.6617 (m100) REVERT: G 63 ARG cc_start: 0.8132 (mmt-90) cc_final: 0.7639 (mmm-85) REVERT: G 113 HIS cc_start: 0.9009 (t-170) cc_final: 0.8186 (t-170) REVERT: G 125 GLN cc_start: 0.9176 (mt0) cc_final: 0.8725 (mp10) REVERT: H 30 THR cc_start: 0.9291 (p) cc_final: 0.8705 (t) REVERT: H 88 TYR cc_start: 0.9082 (m-10) cc_final: 0.8859 (m-10) REVERT: I 42 ARG cc_start: 0.9227 (mtm180) cc_final: 0.8828 (ttp-110) REVERT: I 68 ASN cc_start: 0.9393 (m-40) cc_final: 0.8929 (m110) REVERT: I 73 ASN cc_start: 0.9241 (t0) cc_final: 0.8918 (t0) REVERT: I 75 LYS cc_start: 0.9467 (mmtm) cc_final: 0.9045 (mmtp) REVERT: I 87 VAL cc_start: 0.9626 (m) cc_final: 0.9185 (m) REVERT: I 90 ASP cc_start: 0.9153 (t0) cc_final: 0.8371 (t0) REVERT: I 94 ASN cc_start: 0.8868 (t0) cc_final: 0.8205 (m-40) REVERT: I 95 LYS cc_start: 0.9518 (tptt) cc_final: 0.9313 (ttmm) REVERT: J 43 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8870 (mmtm) REVERT: J 44 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8675 (tm-30) REVERT: J 65 ASP cc_start: 0.8625 (t70) cc_final: 0.7947 (t70) REVERT: J 76 ARG cc_start: 0.9309 (ttm110) cc_final: 0.8928 (ttm110) REVERT: J 81 ASN cc_start: 0.8386 (m110) cc_final: 0.8145 (p0) REVERT: J 85 THR cc_start: 0.9047 (p) cc_final: 0.8150 (p) REVERT: J 99 LEU cc_start: 0.9307 (mt) cc_final: 0.9052 (mp) REVERT: K 50 GLU cc_start: 0.8905 (tp30) cc_final: 0.8226 (tp30) REVERT: K 54 TYR cc_start: 0.8386 (m-10) cc_final: 0.8006 (m-10) REVERT: K 65 LEU cc_start: 0.9607 (mm) cc_final: 0.9164 (mp) REVERT: K 79 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7983 (tptm) REVERT: K 84 PHE cc_start: 0.9164 (m-80) cc_final: 0.8825 (m-10) REVERT: K 90 MET cc_start: 0.9017 (mtm) cc_final: 0.8633 (mtt) REVERT: K 93 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8511 (tm-30) REVERT: K 97 GLU cc_start: 0.8990 (tt0) cc_final: 0.8641 (mt-10) REVERT: K 110 CYS cc_start: 0.8802 (t) cc_final: 0.8517 (t) REVERT: K 120 MET cc_start: 0.9495 (mmp) cc_final: 0.9170 (mmm) REVERT: K 123 ASP cc_start: 0.7813 (t0) cc_final: 0.6851 (t70) REVERT: M 36 LYS cc_start: 0.9105 (mttm) cc_final: 0.8839 (pttt) REVERT: M 56 GLU cc_start: 0.9362 (tt0) cc_final: 0.9039 (mt-10) REVERT: M 64 GLU cc_start: 0.9425 (tt0) cc_final: 0.8990 (tm-30) REVERT: M 68 ASN cc_start: 0.9576 (m-40) cc_final: 0.8268 (m-40) REVERT: M 85 LEU cc_start: 0.9614 (tp) cc_final: 0.9405 (tp) REVERT: M 89 ASN cc_start: 0.8994 (m-40) cc_final: 0.8620 (m-40) REVERT: N 44 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9076 (tm-30) REVERT: N 65 ASP cc_start: 0.9267 (t0) cc_final: 0.8916 (t0) REVERT: N 76 ARG cc_start: 0.8862 (ttt90) cc_final: 0.8155 (ttt-90) REVERT: N 80 TYR cc_start: 0.7597 (m-80) cc_final: 0.7210 (m-10) REVERT: N 83 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8229 (mmm-85) REVERT: N 110 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8384 (tp30) REVERT: N 113 LYS cc_start: 0.9410 (tmmt) cc_final: 0.9179 (ttpp) REVERT: L 51 TYR cc_start: 0.8502 (m-80) cc_final: 0.8099 (m-80) REVERT: L 91 LYS cc_start: 0.9286 (tttm) cc_final: 0.8977 (tttt) REVERT: L 98 TYR cc_start: 0.8714 (m-10) cc_final: 0.8347 (m-80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1298 time to fit residues: 62.2331 Evaluate side-chains 297 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS G 55 GLN G 68 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN K 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043011 restraints weight = 77586.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044512 restraints weight = 36874.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045408 restraints weight = 22832.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046100 restraints weight = 16864.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046452 restraints weight = 13822.057| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15271 Z= 0.216 Angle : 0.648 8.094 21915 Z= 0.371 Chirality : 0.039 0.147 2509 Planarity : 0.005 0.076 1765 Dihedral : 29.851 143.053 4372 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1056 helix: 1.62 (0.22), residues: 538 sheet: -1.12 (0.45), residues: 147 loop : -1.32 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 96 TYR 0.057 0.003 TYR L 88 PHE 0.021 0.002 PHE A 206 TRP 0.018 0.002 TRP A 74 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00481 (15271) covalent geometry : angle 0.64846 (21915) hydrogen bonds : bond 0.05627 ( 856) hydrogen bonds : angle 3.83017 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7755 (t60) cc_final: 0.7431 (t60) REVERT: A 81 LEU cc_start: 0.8856 (mt) cc_final: 0.8431 (pp) REVERT: A 134 MET cc_start: 0.7624 (ttp) cc_final: 0.6522 (mpp) REVERT: A 167 TYR cc_start: 0.7106 (m-80) cc_final: 0.6712 (m-80) REVERT: A 265 TYR cc_start: 0.7747 (m-80) cc_final: 0.7248 (m-10) REVERT: A 280 GLU cc_start: 0.8664 (tt0) cc_final: 0.8144 (tt0) REVERT: A 321 TRP cc_start: 0.6878 (m100) cc_final: 0.6575 (m100) REVERT: G 63 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7733 (mmm-85) REVERT: G 113 HIS cc_start: 0.9034 (t-170) cc_final: 0.8153 (t-170) REVERT: G 125 GLN cc_start: 0.9094 (mt0) cc_final: 0.8492 (mp10) REVERT: H 30 THR cc_start: 0.9414 (p) cc_final: 0.8807 (t) REVERT: H 52 GLU cc_start: 0.8967 (pm20) cc_final: 0.8732 (pm20) REVERT: I 68 ASN cc_start: 0.9243 (m-40) cc_final: 0.8949 (m110) REVERT: I 73 ASN cc_start: 0.9267 (t0) cc_final: 0.8928 (t0) REVERT: I 75 LYS cc_start: 0.9469 (mmtm) cc_final: 0.9016 (mmtp) REVERT: I 87 VAL cc_start: 0.9659 (m) cc_final: 0.9382 (m) REVERT: I 90 ASP cc_start: 0.9018 (t0) cc_final: 0.8637 (t0) REVERT: I 94 ASN cc_start: 0.8983 (t0) cc_final: 0.8346 (m-40) REVERT: I 95 LYS cc_start: 0.9582 (tptt) cc_final: 0.9318 (ttmm) REVERT: I 104 GLN cc_start: 0.8888 (mp10) cc_final: 0.8584 (mp10) REVERT: J 43 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8830 (mmtm) REVERT: J 44 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8676 (tm-30) REVERT: J 65 ASP cc_start: 0.8551 (t70) cc_final: 0.8027 (t0) REVERT: J 76 ARG cc_start: 0.9338 (ttm110) cc_final: 0.8984 (ttm110) REVERT: J 85 THR cc_start: 0.9041 (p) cc_final: 0.8830 (p) REVERT: J 97 LEU cc_start: 0.9383 (mt) cc_final: 0.9168 (mt) REVERT: J 99 LEU cc_start: 0.9325 (mt) cc_final: 0.9067 (mp) REVERT: K 50 GLU cc_start: 0.8857 (tp30) cc_final: 0.8265 (tp30) REVERT: K 54 TYR cc_start: 0.8352 (m-10) cc_final: 0.7910 (m-10) REVERT: K 56 LYS cc_start: 0.9348 (tppt) cc_final: 0.9001 (tptp) REVERT: K 68 GLN cc_start: 0.8849 (pp30) cc_final: 0.8641 (pp30) REVERT: K 79 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7999 (tptm) REVERT: K 84 PHE cc_start: 0.9188 (m-80) cc_final: 0.8809 (m-10) REVERT: K 90 MET cc_start: 0.9052 (mtm) cc_final: 0.8554 (mtt) REVERT: K 93 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8507 (tm-30) REVERT: K 97 GLU cc_start: 0.9030 (tt0) cc_final: 0.8613 (mt-10) REVERT: K 110 CYS cc_start: 0.8729 (t) cc_final: 0.8512 (t) REVERT: K 120 MET cc_start: 0.9469 (mmp) cc_final: 0.9159 (mmm) REVERT: K 123 ASP cc_start: 0.7884 (t0) cc_final: 0.6904 (t70) REVERT: M 36 LYS cc_start: 0.9119 (mttm) cc_final: 0.8829 (tttt) REVERT: M 56 GLU cc_start: 0.9374 (tt0) cc_final: 0.9035 (mt-10) REVERT: M 62 ILE cc_start: 0.9675 (mm) cc_final: 0.9282 (tt) REVERT: M 64 GLU cc_start: 0.9420 (tt0) cc_final: 0.8971 (tm-30) REVERT: M 68 ASN cc_start: 0.9542 (m-40) cc_final: 0.8260 (m-40) REVERT: M 89 ASN cc_start: 0.9026 (m-40) cc_final: 0.8809 (m-40) REVERT: N 44 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9020 (tm-30) REVERT: N 65 ASP cc_start: 0.9275 (t0) cc_final: 0.8898 (t0) REVERT: N 76 ARG cc_start: 0.8904 (ttt90) cc_final: 0.8448 (ttt-90) REVERT: N 80 TYR cc_start: 0.7355 (m-80) cc_final: 0.6586 (m-10) REVERT: N 83 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8357 (mmm160) REVERT: N 110 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8426 (tp30) REVERT: N 113 LYS cc_start: 0.9431 (tmmt) cc_final: 0.9168 (ttpp) REVERT: L 43 VAL cc_start: 0.9713 (m) cc_final: 0.9457 (m) REVERT: L 49 LEU cc_start: 0.9450 (mt) cc_final: 0.9008 (mt) REVERT: L 51 TYR cc_start: 0.8492 (m-80) cc_final: 0.8049 (m-80) REVERT: L 91 LYS cc_start: 0.9325 (tttm) cc_final: 0.9037 (tttt) REVERT: L 98 TYR cc_start: 0.8556 (m-10) cc_final: 0.8305 (m-80) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1272 time to fit residues: 61.2503 Evaluate side-chains 288 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN I 68 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN K 125 GLN L 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.042527 restraints weight = 78311.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044021 restraints weight = 37435.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044984 restraints weight = 23285.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045627 restraints weight = 17036.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045972 restraints weight = 14033.892| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15271 Z= 0.227 Angle : 0.666 8.724 21915 Z= 0.381 Chirality : 0.039 0.172 2509 Planarity : 0.005 0.071 1765 Dihedral : 29.880 138.943 4372 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.11 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1056 helix: 1.36 (0.22), residues: 534 sheet: -1.10 (0.46), residues: 147 loop : -1.25 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 96 TYR 0.046 0.003 TYR H 88 PHE 0.022 0.002 PHE K 67 TRP 0.017 0.002 TRP A 74 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00506 (15271) covalent geometry : angle 0.66612 (21915) hydrogen bonds : bond 0.05770 ( 856) hydrogen bonds : angle 3.94955 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.29 seconds wall clock time: 45 minutes 22.27 seconds (2722.27 seconds total)