Starting phenix.real_space_refine on Fri Feb 14 00:48:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3q_13182/02_2025/7p3q_13182_neut.cif" } resolution = 3.12 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= -0.001 sd= 0.083 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 48 5.49 5 S 64 5.16 5 C 5756 2.51 5 N 1808 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9632 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1139 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 46.349 87.581 52.926 1.00 65.22 S ATOM 48 SG CYS A 6 46.500 91.393 52.216 1.00 66.49 S ATOM 254 SG CYS A 31 43.952 90.097 54.511 1.00 64.58 S ATOM 275 SG CYS A 34 43.720 89.269 50.772 1.00 65.50 S ATOM 4604 SG CYS B 3 50.768 31.995 13.583 1.00107.26 S ATOM 4628 SG CYS B 6 47.797 33.059 11.728 1.00108.81 S ATOM 4834 SG CYS B 31 49.782 29.863 10.657 1.00111.23 S ATOM 4855 SG CYS B 34 51.105 33.063 9.751 1.00113.83 S Restraints were copied for chains: D, F, H, C, E, G Time building chain proxies: 4.58, per 1000 atoms: 0.48 Number of scatterers: 9632 At special positions: 0 Unit cell: (85.05, 101.43, 92.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 64 16.00 P 48 15.00 O 1948 8.00 N 1808 7.00 C 5756 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 6 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 31 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 34 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 3 " pdb=" ZN F 203 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 31 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 6 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 3 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 34 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 6 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 31 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 34 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 3 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 3 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 34 " Number of angles added : 48 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 53.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.788A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.765A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 3.787A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.764A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.922A pdb=" N VAL E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix removed outlier: 3.788A pdb=" N GLU E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.765A pdb=" N PHE E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 96 removed outlier: 3.839A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.788A pdb=" N GLU G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 133 through 147 removed outlier: 3.764A pdb=" N PHE G 137 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.845A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Proline residue: B 112 - end of helix removed outlier: 4.538A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.659A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.846A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Proline residue: D 112 - end of helix removed outlier: 4.538A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.845A pdb=" N GLY F 96 " --> pdb=" O VAL F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 Proline residue: F 112 - end of helix removed outlier: 4.538A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.846A pdb=" N GLY H 96 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 117 Proline residue: H 112 - end of helix removed outlier: 4.538A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 133 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 41 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN D 30 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL D 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 41 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 30 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL E 13 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN E 30 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN H 30 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL H 13 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL G 13 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN G 30 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 41 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN F 30 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL F 13 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET B 47 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.396A pdb=" N MET D 47 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET F 47 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET H 47 " --> pdb=" O LEU H 100 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 3.02 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: 1745 1.32 - 1.45: 2424 1.45 - 1.57: 5455 1.57 - 1.70: 80 1.70 - 1.82: 80 Bond restraints: 9784 Sorted by residual: bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.15e+01 bond pdb=" CA SER E 126 " pdb=" CB SER E 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.14e+01 bond pdb=" CA SER C 126 " pdb=" CB SER C 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.14e+01 bond pdb=" CA SER G 126 " pdb=" CB SER G 126 " ideal model delta sigma weight residual 1.528 1.455 0.073 1.59e-02 3.96e+03 2.12e+01 bond pdb=" N GLY D 111 " pdb=" CA GLY D 111 " ideal model delta sigma weight residual 1.444 1.483 -0.040 8.80e-03 1.29e+04 2.02e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11470 1.76 - 3.53: 1448 3.53 - 5.29: 298 5.29 - 7.05: 91 7.05 - 8.81: 29 Bond angle restraints: 13336 Sorted by residual: angle pdb=" N ASP G 21 " pdb=" CA ASP G 21 " pdb=" C ASP G 21 " ideal model delta sigma weight residual 113.41 104.60 8.81 1.22e+00 6.72e-01 5.22e+01 angle pdb=" N ASP C 21 " pdb=" CA ASP C 21 " pdb=" C ASP C 21 " ideal model delta sigma weight residual 113.41 104.61 8.80 1.22e+00 6.72e-01 5.20e+01 angle pdb=" N ASP A 21 " pdb=" CA ASP A 21 " pdb=" C ASP A 21 " ideal model delta sigma weight residual 113.41 104.62 8.79 1.22e+00 6.72e-01 5.19e+01 angle pdb=" N ASP E 21 " pdb=" CA ASP E 21 " pdb=" C ASP E 21 " ideal model delta sigma weight residual 113.41 104.65 8.76 1.22e+00 6.72e-01 5.15e+01 angle pdb=" C5' DTP E 202 " pdb=" O5' DTP E 202 " pdb=" PA DTP E 202 " ideal model delta sigma weight residual 121.27 127.74 -6.47 1.00e+00 1.00e+00 4.18e+01 ... (remaining 13331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5244 16.82 - 33.64: 668 33.64 - 50.45: 200 50.45 - 67.27: 88 67.27 - 84.09: 48 Dihedral angle restraints: 6248 sinusoidal: 2840 harmonic: 3408 Sorted by residual: dihedral pdb=" C THR A 43 " pdb=" N THR A 43 " pdb=" CA THR A 43 " pdb=" CB THR A 43 " ideal model delta harmonic sigma weight residual -122.00 -113.69 -8.31 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C THR C 43 " pdb=" N THR C 43 " pdb=" CA THR C 43 " pdb=" CB THR C 43 " ideal model delta harmonic sigma weight residual -122.00 -113.71 -8.29 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C THR E 43 " pdb=" N THR E 43 " pdb=" CA THR E 43 " pdb=" CB THR E 43 " ideal model delta harmonic sigma weight residual -122.00 -113.72 -8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1028 0.056 - 0.113: 318 0.113 - 0.169: 95 0.169 - 0.226: 51 0.226 - 0.282: 16 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CA ILE E 25 " pdb=" N ILE E 25 " pdb=" C ILE E 25 " pdb=" CB ILE E 25 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE C 25 " pdb=" N ILE C 25 " pdb=" C ILE C 25 " pdb=" CB ILE C 25 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1505 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 1 " -0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C MET A 1 " 0.087 2.00e-02 2.50e+03 pdb=" O MET A 1 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS A 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 1 " 0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C MET C 1 " -0.087 2.00e-02 2.50e+03 pdb=" O MET C 1 " 0.034 2.00e-02 2.50e+03 pdb=" N HIS C 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 1 " -0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C MET G 1 " 0.087 2.00e-02 2.50e+03 pdb=" O MET G 1 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS G 2 " -0.029 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1229 2.75 - 3.29: 9768 3.29 - 3.83: 16651 3.83 - 4.36: 20979 4.36 - 4.90: 34206 Nonbonded interactions: 82833 Sorted by model distance: nonbonded pdb=" NH1 ARG D 26 " pdb=" OG1 THR D 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG B 26 " pdb=" OG1 THR B 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG H 26 " pdb=" OG1 THR H 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG F 26 " pdb=" OG1 THR F 39 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" OE2 GLU D 42 " model vdw 2.309 3.040 ... (remaining 82828 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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: 1.490 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.040 Find NCS groups from input model: 0.180 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.009 0.074 9784 Z= 0.585 Angle : 1.342 8.814 13336 Z= 0.968 Chirality : 0.070 0.282 1508 Planarity : 0.008 0.052 1676 Dihedral : 18.914 84.088 4024 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.40 % Allowed : 5.20 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1160 helix: 1.46 (0.23), residues: 556 sheet: 0.04 (0.35), residues: 184 loop : -1.16 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 2 PHE 0.027 0.004 PHE G 124 TYR 0.015 0.004 TYR E 121 ARG 0.006 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.7984 (m) cc_final: 0.7534 (p) REVERT: E 43 THR cc_start: 0.7774 (m) cc_final: 0.7374 (p) outliers start: 4 outliers final: 0 residues processed: 207 average time/residue: 0.2721 time to fit residues: 74.1920 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153335 restraints weight = 9437.277| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.09 r_work: 0.3484 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9784 Z= 0.219 Angle : 0.580 5.925 13336 Z= 0.305 Chirality : 0.039 0.129 1508 Planarity : 0.006 0.066 1676 Dihedral : 18.780 87.490 1840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.80 % Allowed : 13.10 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1160 helix: 2.12 (0.22), residues: 556 sheet: 0.41 (0.35), residues: 168 loop : -0.83 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 2 PHE 0.011 0.002 PHE H 38 TYR 0.010 0.002 TYR E 121 ARG 0.009 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7480 (ttm170) cc_final: 0.6748 (tmt170) REVERT: A 43 THR cc_start: 0.8267 (m) cc_final: 0.7849 (p) REVERT: C 42 GLU cc_start: 0.7763 (tt0) cc_final: 0.7473 (pt0) REVERT: C 115 GLU cc_start: 0.7896 (mp0) cc_final: 0.7578 (mp0) REVERT: G 43 THR cc_start: 0.7865 (m) cc_final: 0.7591 (p) REVERT: D 26 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7329 (mmm160) REVERT: F 26 ARG cc_start: 0.7395 (mmm160) cc_final: 0.7177 (mmm160) outliers start: 8 outliers final: 7 residues processed: 178 average time/residue: 0.2913 time to fit residues: 69.3703 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** C 114 GLN G 30 GLN ** G 114 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 = 0.4076 r_free = 0.4076 target = 0.189151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142146 restraints weight = 9600.320| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.01 r_work: 0.3325 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9784 Z= 0.438 Angle : 0.631 6.389 13336 Z= 0.327 Chirality : 0.042 0.137 1508 Planarity : 0.006 0.061 1676 Dihedral : 17.684 86.305 1840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 15.50 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1160 helix: 1.45 (0.22), residues: 584 sheet: -0.02 (0.32), residues: 172 loop : -0.74 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 2 PHE 0.021 0.003 PHE G 124 TYR 0.013 0.003 TYR E 128 ARG 0.011 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.084 Fit side-chains REVERT: A 17 ARG cc_start: 0.7411 (ttm170) cc_final: 0.6793 (tmt170) REVERT: C 25 ILE cc_start: 0.8767 (mt) cc_final: 0.8290 (mt) REVERT: C 42 GLU cc_start: 0.7993 (tt0) cc_final: 0.7496 (pt0) REVERT: C 115 GLU cc_start: 0.7933 (mp0) cc_final: 0.7634 (mp0) REVERT: C 128 TYR cc_start: 0.8412 (t80) cc_final: 0.8164 (t80) REVERT: E 1 MET cc_start: 0.7865 (ptp) cc_final: 0.7500 (ptp) REVERT: G 43 THR cc_start: 0.8317 (m) cc_final: 0.7997 (p) REVERT: D 26 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7397 (mmm160) REVERT: F 42 GLU cc_start: 0.8682 (tm-30) cc_final: 0.7597 (tm-30) REVERT: H 42 GLU cc_start: 0.8688 (tm-30) cc_final: 0.7382 (tm-30) outliers start: 19 outliers final: 15 residues processed: 185 average time/residue: 0.2652 time to fit residues: 66.1714 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146806 restraints weight = 9499.772| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.00 r_work: 0.3394 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9784 Z= 0.233 Angle : 0.529 7.095 13336 Z= 0.278 Chirality : 0.039 0.135 1508 Planarity : 0.005 0.052 1676 Dihedral : 16.430 87.016 1840 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.00 % Allowed : 17.90 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1160 helix: 1.48 (0.23), residues: 572 sheet: 0.12 (0.32), residues: 172 loop : -0.48 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 2 PHE 0.014 0.002 PHE A 124 TYR 0.011 0.002 TYR E 128 ARG 0.004 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 1.283 Fit side-chains REVERT: A 1 MET cc_start: 0.7362 (ptp) cc_final: 0.6921 (ptp) REVERT: A 17 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6841 (tmt170) REVERT: A 37 ARG cc_start: 0.8025 (mpt180) cc_final: 0.7769 (mpt-90) REVERT: C 1 MET cc_start: 0.7616 (ptp) cc_final: 0.7221 (ptp) REVERT: C 17 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7289 (ttm110) REVERT: C 42 GLU cc_start: 0.7923 (tt0) cc_final: 0.7571 (pt0) REVERT: C 115 GLU cc_start: 0.7954 (mp0) cc_final: 0.7695 (mp0) REVERT: E 1 MET cc_start: 0.7804 (ptp) cc_final: 0.7256 (ptp) REVERT: E 42 GLU cc_start: 0.7863 (tt0) cc_final: 0.7578 (tt0) REVERT: G 1 MET cc_start: 0.7637 (ptp) cc_final: 0.7069 (ptp) REVERT: G 43 THR cc_start: 0.8326 (m) cc_final: 0.8064 (p) REVERT: B 42 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 26 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7430 (mmm160) REVERT: D 42 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 26 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7001 (mmm160) REVERT: F 42 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 26 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7173 (mmm160) REVERT: H 42 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 10 outliers final: 9 residues processed: 180 average time/residue: 0.2751 time to fit residues: 65.6670 Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 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 = 0.4028 r_free = 0.4028 target = 0.184698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136955 restraints weight = 9458.893| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.98 r_work: 0.3291 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 9784 Z= 0.529 Angle : 0.640 6.382 13336 Z= 0.329 Chirality : 0.043 0.130 1508 Planarity : 0.006 0.054 1676 Dihedral : 17.160 89.549 1840 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.20 % Allowed : 18.00 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1160 helix: 1.29 (0.22), residues: 580 sheet: -0.05 (0.32), residues: 172 loop : -0.64 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 2 PHE 0.020 0.003 PHE C 124 TYR 0.021 0.003 TYR G 128 ARG 0.009 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7896 (ptp) cc_final: 0.7537 (ptp) REVERT: A 17 ARG cc_start: 0.7406 (ttm170) cc_final: 0.6865 (tmt170) REVERT: C 1 MET cc_start: 0.8079 (ptp) cc_final: 0.7675 (ptp) REVERT: C 25 ILE cc_start: 0.8888 (mt) cc_final: 0.8516 (mm) REVERT: C 42 GLU cc_start: 0.7979 (tt0) cc_final: 0.7652 (pt0) REVERT: E 1 MET cc_start: 0.8173 (ptp) cc_final: 0.7690 (ptp) REVERT: G 1 MET cc_start: 0.8055 (ptp) cc_final: 0.7557 (ptp) REVERT: G 43 THR cc_start: 0.8586 (m) cc_final: 0.8306 (p) REVERT: B 42 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 26 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7451 (mmm160) REVERT: D 42 GLU cc_start: 0.8772 (tm-30) cc_final: 0.7803 (tm-30) REVERT: F 26 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.6974 (mmm160) REVERT: F 42 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7948 (tm-30) REVERT: H 26 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7150 (mmm160) REVERT: H 42 GLU cc_start: 0.8666 (tm-30) cc_final: 0.7737 (tm-30) outliers start: 22 outliers final: 17 residues processed: 183 average time/residue: 0.2711 time to fit residues: 65.9592 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.192641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147123 restraints weight = 9447.887| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.96 r_work: 0.3428 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9784 Z= 0.192 Angle : 0.524 8.074 13336 Z= 0.276 Chirality : 0.039 0.149 1508 Planarity : 0.005 0.055 1676 Dihedral : 15.337 83.136 1840 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.60 % Allowed : 19.30 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1160 helix: 1.38 (0.23), residues: 572 sheet: 0.15 (0.32), residues: 172 loop : -0.46 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 2 PHE 0.009 0.002 PHE C 124 TYR 0.019 0.002 TYR E 121 ARG 0.007 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7525 (ptp) cc_final: 0.6862 (ptp) REVERT: A 17 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6884 (tmt170) REVERT: C 1 MET cc_start: 0.7772 (ptp) cc_final: 0.7342 (ptp) REVERT: C 17 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6827 (tmt170) REVERT: C 25 ILE cc_start: 0.8903 (mt) cc_final: 0.8533 (mm) REVERT: E 1 MET cc_start: 0.7902 (ptp) cc_final: 0.7422 (ptp) REVERT: E 25 ILE cc_start: 0.8955 (mt) cc_final: 0.8664 (mm) REVERT: G 1 MET cc_start: 0.7690 (ptp) cc_final: 0.7169 (ptp) REVERT: G 43 THR cc_start: 0.8489 (m) cc_final: 0.8272 (p) REVERT: B 26 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7429 (mmm160) REVERT: B 42 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 42 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7926 (tm-30) REVERT: F 26 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6984 (mmm160) REVERT: F 42 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 26 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7095 (mmm160) REVERT: H 42 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7746 (tm-30) outliers start: 6 outliers final: 5 residues processed: 168 average time/residue: 0.2763 time to fit residues: 61.3092 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146998 restraints weight = 9500.905| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.97 r_work: 0.3366 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9784 Z= 0.270 Angle : 0.548 6.575 13336 Z= 0.284 Chirality : 0.040 0.160 1508 Planarity : 0.005 0.052 1676 Dihedral : 15.059 76.895 1840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.70 % Allowed : 19.50 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1160 helix: 1.42 (0.22), residues: 580 sheet: 0.23 (0.32), residues: 172 loop : -0.58 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 2 PHE 0.012 0.002 PHE C 124 TYR 0.018 0.003 TYR E 121 ARG 0.007 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6900 (tmt170) REVERT: C 1 MET cc_start: 0.7783 (ptp) cc_final: 0.7305 (ptp) REVERT: C 17 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6765 (tmm160) REVERT: E 1 MET cc_start: 0.7974 (ptp) cc_final: 0.7627 (ptp) REVERT: E 17 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6879 (tmm160) REVERT: E 25 ILE cc_start: 0.8965 (mt) cc_final: 0.8648 (mm) REVERT: G 1 MET cc_start: 0.7769 (ptp) cc_final: 0.7395 (ptp) REVERT: G 43 THR cc_start: 0.8550 (m) cc_final: 0.8317 (p) REVERT: B 26 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7445 (mmm160) REVERT: B 42 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7657 (tm-30) REVERT: F 26 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.6992 (mmm160) REVERT: F 42 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7975 (tm-30) REVERT: H 26 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7098 (mmm160) REVERT: H 42 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7920 (tm-30) outliers start: 7 outliers final: 6 residues processed: 160 average time/residue: 0.2561 time to fit residues: 54.8578 Evaluate side-chains 162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 95 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.191887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146068 restraints weight = 9517.480| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.95 r_work: 0.3369 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9784 Z= 0.257 Angle : 0.540 6.741 13336 Z= 0.281 Chirality : 0.039 0.153 1508 Planarity : 0.005 0.053 1676 Dihedral : 14.514 81.929 1840 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.80 % Allowed : 19.80 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1160 helix: 1.41 (0.22), residues: 572 sheet: 0.25 (0.32), residues: 172 loop : -0.37 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 2 PHE 0.009 0.002 PHE C 124 TYR 0.019 0.003 TYR C 121 ARG 0.007 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7303 (ttm170) cc_final: 0.6822 (tmt170) REVERT: C 1 MET cc_start: 0.7746 (ptp) cc_final: 0.7295 (ptp) REVERT: C 17 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6761 (tmm160) REVERT: C 43 THR cc_start: 0.8239 (m) cc_final: 0.7935 (p) REVERT: E 1 MET cc_start: 0.7991 (ptp) cc_final: 0.7601 (ptp) REVERT: E 17 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6821 (tmm160) REVERT: E 25 ILE cc_start: 0.8955 (mt) cc_final: 0.8639 (mm) REVERT: G 1 MET cc_start: 0.7742 (ptp) cc_final: 0.7332 (ptp) REVERT: G 17 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7064 (tmt170) REVERT: B 42 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7444 (tm-30) REVERT: D 42 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7927 (tm-30) REVERT: F 26 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6935 (mmm160) REVERT: F 42 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7871 (tm-30) REVERT: H 26 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7259 (mmm160) REVERT: H 42 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7938 (tm-30) outliers start: 8 outliers final: 7 residues processed: 156 average time/residue: 0.2607 time to fit residues: 54.8569 Evaluate side-chains 158 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146454 restraints weight = 9480.459| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.96 r_work: 0.3402 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9784 Z= 0.207 Angle : 0.532 7.068 13336 Z= 0.276 Chirality : 0.039 0.161 1508 Planarity : 0.004 0.051 1676 Dihedral : 14.017 89.403 1840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.60 % Allowed : 20.90 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1160 helix: 1.46 (0.22), residues: 572 sheet: 0.49 (0.32), residues: 168 loop : -0.36 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 2 PHE 0.008 0.002 PHE B 38 TYR 0.019 0.002 TYR E 121 ARG 0.011 0.000 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7223 (ttm170) cc_final: 0.6903 (tmt170) REVERT: C 17 ARG cc_start: 0.7174 (ttm110) cc_final: 0.6877 (tmm160) REVERT: C 43 THR cc_start: 0.8239 (m) cc_final: 0.8005 (p) REVERT: E 1 MET cc_start: 0.7884 (ptp) cc_final: 0.7508 (ptp) REVERT: E 17 ARG cc_start: 0.7335 (ttm110) cc_final: 0.6948 (tmm160) REVERT: E 25 ILE cc_start: 0.8983 (mt) cc_final: 0.8672 (mm) REVERT: G 1 MET cc_start: 0.7634 (ptp) cc_final: 0.7280 (ptp) REVERT: G 17 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7150 (tmt170) REVERT: D 42 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7794 (tm-30) REVERT: F 26 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7022 (mmm160) REVERT: F 42 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7759 (tm-30) REVERT: H 26 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7301 (mmm160) REVERT: H 42 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7948 (tm-30) outliers start: 6 outliers final: 6 residues processed: 152 average time/residue: 0.2561 time to fit residues: 52.1422 Evaluate side-chains 154 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.192823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146789 restraints weight = 9535.821| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.98 r_work: 0.3407 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9784 Z= 0.205 Angle : 0.532 6.847 13336 Z= 0.276 Chirality : 0.038 0.160 1508 Planarity : 0.004 0.051 1676 Dihedral : 13.596 87.519 1840 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.60 % Allowed : 20.70 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1160 helix: 1.41 (0.22), residues: 588 sheet: 0.49 (0.32), residues: 168 loop : -0.45 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 2 PHE 0.008 0.001 PHE C 124 TYR 0.020 0.002 TYR C 121 ARG 0.008 0.000 ARG D 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7204 (ttm170) cc_final: 0.6905 (tmt170) REVERT: C 17 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6904 (tmm160) REVERT: C 43 THR cc_start: 0.8140 (m) cc_final: 0.7923 (p) REVERT: E 1 MET cc_start: 0.7835 (ptp) cc_final: 0.7469 (ptp) REVERT: E 17 ARG cc_start: 0.7358 (ttm110) cc_final: 0.6983 (tmm160) REVERT: E 25 ILE cc_start: 0.8989 (mt) cc_final: 0.8656 (mm) REVERT: G 1 MET cc_start: 0.7583 (ptp) cc_final: 0.7244 (ptp) REVERT: B 42 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 42 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 26 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7036 (mmm160) REVERT: F 42 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7764 (tm-30) REVERT: H 26 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7277 (mmm160) REVERT: H 42 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7960 (tm-30) outliers start: 6 outliers final: 6 residues processed: 152 average time/residue: 0.2603 time to fit residues: 53.4807 Evaluate side-chains 155 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 0.0000 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.196257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151055 restraints weight = 9537.646| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.96 r_work: 0.3447 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.183 Angle : 0.525 7.067 13336 Z= 0.272 Chirality : 0.038 0.160 1508 Planarity : 0.004 0.050 1676 Dihedral : 13.259 87.181 1840 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.60 % Allowed : 20.80 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1160 helix: 1.48 (0.22), residues: 588 sheet: 0.51 (0.31), residues: 168 loop : -0.40 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 2 PHE 0.007 0.001 PHE B 38 TYR 0.020 0.002 TYR G 121 ARG 0.007 0.000 ARG B 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5338.96 seconds wall clock time: 95 minutes 25.74 seconds (5725.74 seconds total)