Starting phenix.real_space_refine on Tue Jul 29 19:13:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.map" model { file = "/net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7s_52660/07_2025/9i7s_52660.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 34 5.16 5 C 7316 2.51 5 N 1817 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11338 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "E" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "G" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "K" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'DU0': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'DU0': 2, 'PC1': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'DU0': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Restraints were copied for chains: B, F, H, J, L Time building chain proxies: 11.80, per 1000 atoms: 1.04 Number of scatterers: 11338 At special positions: 0 Unit cell: (128.925, 148.407, 107.724, 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 34 16.00 P 11 15.00 O 2160 8.00 N 1817 7.00 C 7316 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.5 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 51.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.716A pdb=" N LEU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 117 Proline residue: C 100 - end of helix Processing helix chain 'E' and resid 11 through 50 Proline residue: E 40 - end of helix removed outlier: 4.036A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.636A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 48 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'I' and resid 23 through 57 removed outlier: 5.496A pdb=" N LEU I 46 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.577A pdb=" N LEU I 67 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 36 Processing helix chain 'K' and resid 36 through 80 removed outlier: 3.551A pdb=" N GLU K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 104 removed outlier: 3.502A pdb=" N ALA K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 108 through 123 Processing helix chain 'K' and resid 125 through 137 Processing helix chain 'K' and resid 138 through 152 removed outlier: 3.709A pdb=" N ILE K 144 " --> pdb=" O PRO K 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.299A pdb=" N GLU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 335' Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 45 through 56 removed outlier: 3.716A pdb=" N LEU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 117 Proline residue: D 100 - end of helix Processing helix chain 'F' and resid 11 through 50 Proline residue: F 40 - end of helix removed outlier: 4.036A pdb=" N PHE F 50 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 26 removed outlier: 3.636A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'J' and resid 23 through 57 removed outlier: 5.496A pdb=" N LEU J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Proline residue: J 47 - end of helix Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.577A pdb=" N LEU J 67 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 36 Processing helix chain 'L' and resid 36 through 80 removed outlier: 3.551A pdb=" N GLU L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 104 removed outlier: 3.502A pdb=" N ALA L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 108 through 123 Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 138 through 152 removed outlier: 3.709A pdb=" N ILE L 144 " --> pdb=" O PRO L 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 331 through 335 removed outlier: 4.299A pdb=" N GLU B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73 removed outlier: 6.357A pdb=" N PHE A 78 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA A 146 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 174 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73 removed outlier: 6.357A pdb=" N PHE B 78 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA B 146 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 174 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1860 1.32 - 1.44: 3000 1.44 - 1.56: 6631 1.56 - 1.69: 28 1.69 - 1.81: 64 Bond restraints: 11583 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO F 8 " pdb=" CG PRO F 8 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO E 10 " pdb=" CG PRO E 10 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.43e+00 bond pdb=" CB PRO F 10 " pdb=" CG PRO F 10 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.43e+00 bond pdb=" CB PRO G 16 " pdb=" CG PRO G 16 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.86e+00 ... (remaining 11578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 15308 2.25 - 4.49: 343 4.49 - 6.74: 46 6.74 - 8.98: 0 8.98 - 11.23: 4 Bond angle restraints: 15701 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" N ASP A 338 " pdb=" CA ASP A 338 " pdb=" C ASP A 338 " ideal model delta sigma weight residual 112.38 117.06 -4.68 1.22e+00 6.72e-01 1.47e+01 angle pdb=" N ASP B 338 " pdb=" CA ASP B 338 " pdb=" C ASP B 338 " ideal model delta sigma weight residual 112.38 117.06 -4.68 1.22e+00 6.72e-01 1.47e+01 angle pdb=" CA PRO F 12 " pdb=" N PRO F 12 " pdb=" CD PRO F 12 " ideal model delta sigma weight residual 112.00 107.32 4.68 1.40e+00 5.10e-01 1.12e+01 ... (remaining 15696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 7222 24.33 - 48.65: 247 48.65 - 72.98: 88 72.98 - 97.31: 32 97.31 - 121.63: 32 Dihedral angle restraints: 7621 sinusoidal: 3667 harmonic: 3954 Sorted by residual: dihedral pdb=" C09 DU0 B 403 " pdb=" C11 DU0 B 403 " pdb=" O10 DU0 B 403 " pdb=" C12 DU0 B 403 " ideal model delta sinusoidal sigma weight residual 58.49 -63.14 121.63 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C09 DU0 A 403 " pdb=" C11 DU0 A 403 " pdb=" O10 DU0 A 403 " pdb=" C12 DU0 A 403 " ideal model delta sinusoidal sigma weight residual 58.49 -63.14 121.63 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C09 DU0 H 101 " pdb=" C11 DU0 H 101 " pdb=" O10 DU0 H 101 " pdb=" C12 DU0 H 101 " ideal model delta sinusoidal sigma weight residual 58.49 -61.95 120.44 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 7618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1241 0.048 - 0.095: 362 0.095 - 0.143: 98 0.143 - 0.190: 18 0.190 - 0.238: 8 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" C PRO E 40 " pdb=" CB PRO E 40 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" C PRO F 40 " pdb=" CB PRO F 40 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASP B 338 " pdb=" N ASP B 338 " pdb=" C ASP B 338 " pdb=" CB ASP B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1724 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 39 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO E 40 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 39 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO F 40 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO F 40 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F 40 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 11 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO E 12 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO E 12 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 12 " -0.057 5.00e-02 4.00e+02 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.26: 10783 3.26 - 3.80: 16975 3.80 - 4.35: 21831 4.35 - 4.90: 38539 Nonbonded interactions: 88404 Sorted by model distance: nonbonded pdb=" NE2 GLN A 147 " pdb=" OE2 GLU A 149 " model vdw 2.160 3.120 nonbonded pdb=" NE2 GLN B 147 " pdb=" OE2 GLU B 149 " model vdw 2.160 3.120 nonbonded pdb=" NH2 ARG B 301 " pdb=" O ALA B 304 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG A 301 " pdb=" O ALA A 304 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR D 105 " pdb=" O14 PC1 D 403 " model vdw 2.245 3.040 ... (remaining 88399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 347 or resid 401 through 403)) selection = (chain 'B' and (resid 21 through 347 or resid 401 through 403)) } ncs_group { reference = (chain 'C' and (resid 28 through 118 or (resid 201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 203 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C3A or name C3B or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 28 through 118 or (resid 401 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 403 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C3A or name C3B or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 10.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.850 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 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 : 0.006 0.092 11585 Z= 0.265 Angle : 0.779 11.228 15701 Z= 0.404 Chirality : 0.051 0.238 1727 Planarity : 0.010 0.115 1930 Dihedral : 17.287 121.631 5069 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.54 % Allowed : 1.26 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1330 helix: 1.60 (0.19), residues: 642 sheet: 0.99 (0.26), residues: 400 loop : -0.08 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 197 HIS 0.006 0.002 HIS B 316 PHE 0.017 0.002 PHE K 91 TYR 0.016 0.002 TYR B 237 ARG 0.019 0.003 ARG L 44 Details of bonding type rmsd hydrogen bonds : bond 0.18761 ( 808) hydrogen bonds : angle 7.04566 ( 2358) covalent geometry : bond 0.00635 (11583) covalent geometry : angle 0.77874 (15701) Misc. bond : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 48 SER cc_start: 0.9178 (p) cc_final: 0.8913 (p) REVERT: I 56 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7976 (mtt90) REVERT: A 111 ASP cc_start: 0.7817 (m-30) cc_final: 0.7591 (m-30) REVERT: A 143 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: A 156 ASP cc_start: 0.8728 (p0) cc_final: 0.8063 (p0) REVERT: A 217 LYS cc_start: 0.8592 (tttp) cc_final: 0.8341 (ttmt) REVERT: A 289 ASP cc_start: 0.8335 (p0) cc_final: 0.8070 (p0) REVERT: A 307 MET cc_start: 0.8452 (ttp) cc_final: 0.8233 (ttm) REVERT: A 328 SER cc_start: 0.8472 (m) cc_final: 0.8243 (t) REVERT: H 48 SER cc_start: 0.9178 (p) cc_final: 0.8914 (p) REVERT: J 56 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7975 (mtt90) REVERT: B 111 ASP cc_start: 0.7819 (m-30) cc_final: 0.7592 (m-30) REVERT: B 143 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: B 156 ASP cc_start: 0.8725 (p0) cc_final: 0.8058 (p0) REVERT: B 217 LYS cc_start: 0.8589 (tttp) cc_final: 0.8341 (ttmt) REVERT: B 289 ASP cc_start: 0.8337 (p0) cc_final: 0.8070 (p0) REVERT: B 307 MET cc_start: 0.8458 (ttp) cc_final: 0.8238 (ttm) REVERT: B 328 SER cc_start: 0.8474 (m) cc_final: 0.8244 (t) outliers start: 6 outliers final: 0 residues processed: 200 average time/residue: 0.3064 time to fit residues: 80.4287 Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.217847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135503 restraints weight = 12343.561| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.35 r_work: 0.3369 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11585 Z= 0.169 Angle : 0.677 12.068 15701 Z= 0.333 Chirality : 0.043 0.196 1727 Planarity : 0.005 0.054 1930 Dihedral : 13.235 101.639 2587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.90 % Allowed : 6.41 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1330 helix: 2.54 (0.19), residues: 652 sheet: 0.99 (0.26), residues: 398 loop : 0.70 (0.46), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.003 0.001 HIS B 150 PHE 0.012 0.001 PHE L 116 TYR 0.020 0.001 TYR K 117 ARG 0.007 0.001 ARG K 44 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 808) hydrogen bonds : angle 4.82054 ( 2358) covalent geometry : bond 0.00375 (11583) covalent geometry : angle 0.67678 (15701) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.7928 (ptm) cc_final: 0.7727 (ptp) REVERT: K 147 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: K 148 MET cc_start: 0.4221 (tmm) cc_final: 0.3217 (ttm) REVERT: A 143 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6271 (tp40) REVERT: D 56 MET cc_start: 0.7924 (ptm) cc_final: 0.7723 (ptp) REVERT: L 147 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: L 148 MET cc_start: 0.4215 (tmm) cc_final: 0.3209 (ttm) REVERT: B 143 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6265 (tp40) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2246 time to fit residues: 36.8186 Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 92 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.216455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137244 restraints weight = 12187.108| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.12 r_work: 0.3388 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11585 Z= 0.124 Angle : 0.564 10.942 15701 Z= 0.284 Chirality : 0.040 0.164 1727 Planarity : 0.004 0.037 1930 Dihedral : 11.448 98.699 2587 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.62 % Allowed : 8.48 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.24), residues: 1330 helix: 2.80 (0.19), residues: 654 sheet: 0.88 (0.26), residues: 398 loop : 0.63 (0.45), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 64 HIS 0.002 0.001 HIS L 35 PHE 0.008 0.001 PHE K 29 TYR 0.017 0.001 TYR G 21 ARG 0.005 0.000 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 808) hydrogen bonds : angle 4.41696 ( 2358) covalent geometry : bond 0.00278 (11583) covalent geometry : angle 0.56409 (15701) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: K 148 MET cc_start: 0.4195 (tmm) cc_final: 0.3085 (ttp) REVERT: A 143 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6147 (tp40) REVERT: L 147 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: L 148 MET cc_start: 0.4194 (tmm) cc_final: 0.3080 (ttp) REVERT: B 143 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6150 (tp40) outliers start: 18 outliers final: 4 residues processed: 122 average time/residue: 0.1929 time to fit residues: 36.6882 Evaluate side-chains 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.217152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133766 restraints weight = 12410.685| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.35 r_work: 0.3381 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11585 Z= 0.155 Angle : 0.582 11.470 15701 Z= 0.292 Chirality : 0.040 0.145 1727 Planarity : 0.004 0.044 1930 Dihedral : 11.011 96.117 2587 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 9.75 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1330 helix: 2.86 (0.19), residues: 658 sheet: 0.64 (0.26), residues: 404 loop : 0.33 (0.46), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 64 HIS 0.002 0.001 HIS D 51 PHE 0.010 0.001 PHE L 39 TYR 0.017 0.001 TYR H 21 ARG 0.007 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 808) hydrogen bonds : angle 4.37029 ( 2358) covalent geometry : bond 0.00363 (11583) covalent geometry : angle 0.58186 (15701) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: K 148 MET cc_start: 0.4263 (tmm) cc_final: 0.2989 (ttp) REVERT: A 143 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6186 (tp40) REVERT: L 147 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: L 148 MET cc_start: 0.4269 (tmm) cc_final: 0.3003 (ttp) REVERT: B 143 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6195 (tp40) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2041 time to fit residues: 29.5287 Evaluate side-chains 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.215946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136614 restraints weight = 12278.081| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.26 r_work: 0.3326 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11585 Z= 0.150 Angle : 0.563 10.066 15701 Z= 0.285 Chirality : 0.040 0.145 1727 Planarity : 0.004 0.047 1930 Dihedral : 10.579 93.560 2587 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 9.39 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.24), residues: 1330 helix: 2.80 (0.19), residues: 658 sheet: 0.61 (0.26), residues: 402 loop : 0.14 (0.45), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 64 HIS 0.002 0.001 HIS A 150 PHE 0.009 0.001 PHE K 116 TYR 0.018 0.001 TYR H 21 ARG 0.008 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 808) hydrogen bonds : angle 4.30781 ( 2358) covalent geometry : bond 0.00350 (11583) covalent geometry : angle 0.56281 (15701) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: K 148 MET cc_start: 0.4148 (tmm) cc_final: 0.3159 (ttp) REVERT: A 143 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6229 (tp40) REVERT: L 147 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: L 148 MET cc_start: 0.4154 (tmm) cc_final: 0.3167 (ttp) REVERT: B 143 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6234 (tp40) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.2029 time to fit residues: 31.9802 Evaluate side-chains 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.215066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134391 restraints weight = 12250.699| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.10 r_work: 0.3412 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11585 Z= 0.116 Angle : 0.529 9.044 15701 Z= 0.270 Chirality : 0.039 0.141 1727 Planarity : 0.004 0.051 1930 Dihedral : 10.109 91.081 2587 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.99 % Allowed : 9.21 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.24), residues: 1330 helix: 2.99 (0.19), residues: 660 sheet: 0.61 (0.26), residues: 402 loop : 0.06 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.002 0.001 HIS C 51 PHE 0.008 0.001 PHE E 41 TYR 0.019 0.001 TYR H 21 ARG 0.008 0.000 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 808) hydrogen bonds : angle 4.15825 ( 2358) covalent geometry : bond 0.00265 (11583) covalent geometry : angle 0.52885 (15701) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 LEU cc_start: 0.4831 (tp) cc_final: 0.4416 (pp) REVERT: K 147 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: K 148 MET cc_start: 0.4240 (tmm) cc_final: 0.2979 (ttp) REVERT: A 143 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6273 (tp40) REVERT: A 145 MET cc_start: 0.8180 (mtp) cc_final: 0.7548 (mmt) REVERT: L 120 LEU cc_start: 0.4845 (tp) cc_final: 0.4428 (pp) REVERT: L 147 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: L 148 MET cc_start: 0.4246 (tmm) cc_final: 0.2986 (ttp) REVERT: B 143 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6279 (tp40) REVERT: B 145 MET cc_start: 0.8178 (mtp) cc_final: 0.7549 (mmt) outliers start: 22 outliers final: 10 residues processed: 104 average time/residue: 0.1922 time to fit residues: 30.7249 Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 40.0000 chunk 9 optimal weight: 0.3980 chunk 64 optimal weight: 0.3980 chunk 88 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.216627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135806 restraints weight = 12508.761| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.34 r_work: 0.3350 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.128 Angle : 0.530 8.328 15701 Z= 0.271 Chirality : 0.039 0.144 1727 Planarity : 0.004 0.051 1930 Dihedral : 9.921 89.221 2587 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.17 % Allowed : 9.21 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.24), residues: 1330 helix: 3.02 (0.19), residues: 660 sheet: 0.55 (0.26), residues: 406 loop : -0.03 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.002 0.001 HIS C 51 PHE 0.007 0.001 PHE E 41 TYR 0.020 0.001 TYR G 21 ARG 0.009 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 808) hydrogen bonds : angle 4.14556 ( 2358) covalent geometry : bond 0.00298 (11583) covalent geometry : angle 0.52971 (15701) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 LEU cc_start: 0.4861 (tp) cc_final: 0.4484 (pp) REVERT: K 147 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6528 (pm20) REVERT: K 148 MET cc_start: 0.4241 (tmm) cc_final: 0.2940 (ttp) REVERT: A 143 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6227 (tp40) REVERT: A 145 MET cc_start: 0.7942 (mtp) cc_final: 0.7488 (mmt) REVERT: A 156 ASP cc_start: 0.8831 (p0) cc_final: 0.8533 (p0) REVERT: L 120 LEU cc_start: 0.4877 (tp) cc_final: 0.4495 (pp) REVERT: L 147 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: L 148 MET cc_start: 0.4242 (tmm) cc_final: 0.2943 (ttp) REVERT: B 143 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6242 (tp40) REVERT: B 145 MET cc_start: 0.7942 (mtp) cc_final: 0.7486 (mmt) REVERT: B 156 ASP cc_start: 0.8838 (p0) cc_final: 0.8541 (p0) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.1982 time to fit residues: 32.9880 Evaluate side-chains 114 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.214034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132952 restraints weight = 12110.191| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.09 r_work: 0.3400 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.136 Angle : 0.543 9.980 15701 Z= 0.277 Chirality : 0.039 0.144 1727 Planarity : 0.004 0.054 1930 Dihedral : 9.821 87.277 2587 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.99 % Allowed : 9.93 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.24), residues: 1330 helix: 3.10 (0.19), residues: 658 sheet: 0.56 (0.26), residues: 404 loop : -0.08 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.003 0.001 HIS C 51 PHE 0.007 0.001 PHE E 41 TYR 0.020 0.001 TYR G 21 ARG 0.010 0.000 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 808) hydrogen bonds : angle 4.13690 ( 2358) covalent geometry : bond 0.00317 (11583) covalent geometry : angle 0.54254 (15701) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 LEU cc_start: 0.4630 (tp) cc_final: 0.4389 (pp) REVERT: K 147 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6419 (pm20) REVERT: K 148 MET cc_start: 0.4249 (tmm) cc_final: 0.2935 (ttp) REVERT: A 143 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6272 (tp40) REVERT: A 145 MET cc_start: 0.7836 (mtp) cc_final: 0.7494 (mmt) REVERT: L 120 LEU cc_start: 0.4638 (tp) cc_final: 0.4394 (pp) REVERT: L 147 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6428 (pm20) REVERT: L 148 MET cc_start: 0.4247 (tmm) cc_final: 0.2930 (ttp) REVERT: B 143 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6281 (tp40) REVERT: B 145 MET cc_start: 0.7806 (mtp) cc_final: 0.7481 (mmt) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.1897 time to fit residues: 31.9791 Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 0.0020 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.212286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133986 restraints weight = 12188.193| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.25 r_work: 0.3303 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11585 Z= 0.173 Angle : 0.576 9.792 15701 Z= 0.294 Chirality : 0.040 0.147 1727 Planarity : 0.004 0.052 1930 Dihedral : 10.034 86.490 2587 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.90 % Allowed : 9.66 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1330 helix: 3.12 (0.19), residues: 656 sheet: 0.51 (0.26), residues: 404 loop : -0.18 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 221 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.001 PHE D 101 TYR 0.020 0.001 TYR G 21 ARG 0.008 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 808) hydrogen bonds : angle 4.26018 ( 2358) covalent geometry : bond 0.00411 (11583) covalent geometry : angle 0.57614 (15701) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 101 MET cc_start: 0.5081 (ptp) cc_final: 0.4205 (ptt) REVERT: K 120 LEU cc_start: 0.4737 (tp) cc_final: 0.4467 (pp) REVERT: K 147 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: K 148 MET cc_start: 0.4224 (tmm) cc_final: 0.2801 (ttm) REVERT: A 143 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6431 (tp40) REVERT: A 145 MET cc_start: 0.7906 (mtp) cc_final: 0.7475 (mmt) REVERT: L 101 MET cc_start: 0.5085 (ptp) cc_final: 0.4210 (ptt) REVERT: L 120 LEU cc_start: 0.4754 (tp) cc_final: 0.4478 (pp) REVERT: L 147 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: L 148 MET cc_start: 0.4216 (tmm) cc_final: 0.2795 (ttm) REVERT: B 143 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6442 (tp40) REVERT: B 145 MET cc_start: 0.7903 (mtp) cc_final: 0.7475 (mmt) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.1942 time to fit residues: 30.7018 Evaluate side-chains 107 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.216375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136850 restraints weight = 12292.880| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.20 r_work: 0.3330 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.133 Angle : 0.537 10.176 15701 Z= 0.274 Chirality : 0.039 0.143 1727 Planarity : 0.004 0.054 1930 Dihedral : 9.796 84.815 2587 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.62 % Allowed : 10.20 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.24), residues: 1330 helix: 3.20 (0.19), residues: 656 sheet: 0.53 (0.26), residues: 404 loop : -0.16 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.002 0.001 HIS B 82 PHE 0.007 0.001 PHE E 41 TYR 0.020 0.001 TYR G 21 ARG 0.009 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 808) hydrogen bonds : angle 4.11839 ( 2358) covalent geometry : bond 0.00316 (11583) covalent geometry : angle 0.53697 (15701) Misc. bond : bond 0.00036 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.8029 (pmm) cc_final: 0.7745 (pmm) REVERT: K 101 MET cc_start: 0.5148 (ptp) cc_final: 0.4158 (ttp) REVERT: K 120 LEU cc_start: 0.4709 (tp) cc_final: 0.4473 (pp) REVERT: K 147 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6450 (pm20) REVERT: K 148 MET cc_start: 0.4184 (tmm) cc_final: 0.2757 (ttm) REVERT: A 143 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6326 (tp40) REVERT: A 145 MET cc_start: 0.7837 (mtp) cc_final: 0.7439 (mmt) REVERT: D 56 MET cc_start: 0.8029 (pmm) cc_final: 0.7742 (pmm) REVERT: L 101 MET cc_start: 0.5162 (ptp) cc_final: 0.4169 (ttp) REVERT: L 120 LEU cc_start: 0.4728 (tp) cc_final: 0.4487 (pp) REVERT: L 147 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: L 148 MET cc_start: 0.4177 (tmm) cc_final: 0.2750 (ttm) REVERT: B 143 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6335 (tp40) REVERT: B 145 MET cc_start: 0.7833 (mtp) cc_final: 0.7436 (mmt) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.2062 time to fit residues: 32.2291 Evaluate side-chains 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 0.0970 chunk 125 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.216507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150410 restraints weight = 12297.826| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.56 r_work: 0.3332 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.128 Angle : 0.532 9.963 15701 Z= 0.270 Chirality : 0.039 0.143 1727 Planarity : 0.004 0.054 1930 Dihedral : 9.635 83.312 2587 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.53 % Allowed : 10.38 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.24), residues: 1330 helix: 3.24 (0.19), residues: 656 sheet: 0.52 (0.26), residues: 404 loop : -0.17 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.002 0.001 HIS A 82 PHE 0.007 0.001 PHE H 45 TYR 0.019 0.001 TYR G 21 ARG 0.009 0.000 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 808) hydrogen bonds : angle 4.06651 ( 2358) covalent geometry : bond 0.00303 (11583) covalent geometry : angle 0.53225 (15701) Misc. bond : bond 0.00038 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7870.64 seconds wall clock time: 137 minutes 5.52 seconds (8225.52 seconds total)