Starting phenix.real_space_refine on Wed Sep 25 05:17:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_13182_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_13182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_13182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_13182_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3q_13182/09_2024/7p3q_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-5461/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: 4.25, per 1000 atoms: 0.44 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 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: 1.11 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: 2.80 Time building geometry restraints manager: 3.05 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 145 or (resid 146 through 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 203)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 145 or (resid 146 through 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 203)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 145 or (resid 146 through 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 203)) selection = chain 'F' selection = (chain 'G' and (resid 1 through 145 or (resid 146 through 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 203)) selection = chain 'H' } 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: 1.780 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: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.230 Find NCS groups from input model: 0.510 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 1.138 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: 0.2650 time to fit residues: 72.3198 Evaluate side-chains 176 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7304 (ttm170) cc_final: 0.7082 (tmt170) REVERT: A 43 THR cc_start: 0.8204 (m) cc_final: 0.7763 (p) REVERT: C 115 GLU cc_start: 0.7808 (mp0) cc_final: 0.7563 (mp0) REVERT: G 43 THR cc_start: 0.7769 (m) cc_final: 0.7468 (p) outliers start: 8 outliers final: 7 residues processed: 178 average time/residue: 0.2580 time to fit residues: 61.4843 Evaluate side-chains 167 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 56 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 30 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9784 Z= 0.417 Angle : 0.629 6.281 13336 Z= 0.327 Chirality : 0.041 0.131 1508 Planarity : 0.006 0.060 1676 Dihedral : 17.701 86.401 1840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.90 % Allowed : 15.70 % Favored : 82.40 % 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: 0.72 (0.25), residues: 1160 helix: 1.48 (0.22), residues: 584 sheet: 0.04 (0.32), residues: 172 loop : -0.75 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 2 PHE 0.020 0.003 PHE G 124 TYR 0.013 0.002 TYR E 128 ARG 0.009 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 fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.073 Fit side-chains REVERT: A 17 ARG cc_start: 0.7298 (ttm170) cc_final: 0.7098 (tmt170) REVERT: C 115 GLU cc_start: 0.7786 (mp0) cc_final: 0.7545 (mp0) REVERT: G 1 MET cc_start: 0.7740 (ptp) cc_final: 0.7383 (ptp) REVERT: G 43 THR cc_start: 0.8211 (m) cc_final: 0.7867 (p) REVERT: B 42 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7140 (tm-30) REVERT: D 26 ARG cc_start: 0.7421 (mmm160) cc_final: 0.6778 (mmm160) REVERT: F 42 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7775 (tm-30) REVERT: H 42 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7636 (tm-30) outliers start: 19 outliers final: 14 residues processed: 185 average time/residue: 0.2485 time to fit residues: 62.3599 Evaluate side-chains 174 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2265 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= 0.183 Angle : 0.517 7.295 13336 Z= 0.274 Chirality : 0.038 0.132 1508 Planarity : 0.005 0.051 1676 Dihedral : 16.176 88.002 1840 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.90 % Allowed : 17.90 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.25), residues: 1160 helix: 1.52 (0.23), residues: 576 sheet: 0.20 (0.33), residues: 172 loop : -0.57 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 2 PHE 0.011 0.002 PHE A 124 TYR 0.014 0.002 TYR C 128 ARG 0.006 0.000 ARG H 26 *********************** 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 177 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 1.064 Fit side-chains REVERT: A 1 MET cc_start: 0.7274 (ptp) cc_final: 0.6888 (ptp) REVERT: E 1 MET cc_start: 0.7542 (ptp) cc_final: 0.7120 (ptp) REVERT: E 42 GLU cc_start: 0.7072 (tt0) cc_final: 0.6828 (tt0) REVERT: G 1 MET cc_start: 0.7528 (ptp) cc_final: 0.7101 (ptp) REVERT: G 43 THR cc_start: 0.8164 (m) cc_final: 0.7874 (p) REVERT: B 42 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7360 (tm-30) REVERT: D 26 ARG cc_start: 0.7395 (mmm160) cc_final: 0.6898 (mmm160) REVERT: D 42 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7331 (tm-30) REVERT: F 26 ARG cc_start: 0.7389 (mmm160) cc_final: 0.7005 (mmm160) REVERT: F 42 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7685 (tm-30) REVERT: H 26 ARG cc_start: 0.7414 (mmm160) cc_final: 0.7194 (mmm160) REVERT: H 42 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 9 outliers final: 8 residues processed: 169 average time/residue: 0.2594 time to fit residues: 58.7336 Evaluate side-chains 167 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 B residue 101 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 9784 Z= 0.558 Angle : 0.660 6.367 13336 Z= 0.338 Chirality : 0.044 0.131 1508 Planarity : 0.006 0.054 1676 Dihedral : 17.199 87.151 1840 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.00 % Allowed : 18.10 % Favored : 79.90 % 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: 0.61 (0.25), residues: 1160 helix: 1.29 (0.23), residues: 580 sheet: -0.01 (0.32), residues: 172 loop : -0.61 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 2 PHE 0.020 0.003 PHE C 124 TYR 0.018 0.003 TYR A 128 ARG 0.007 0.001 ARG F 7 *********************** 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 192 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7853 (ptp) cc_final: 0.7387 (ptp) REVERT: A 17 ARG cc_start: 0.7729 (tmt170) cc_final: 0.7221 (tmm160) REVERT: E 1 MET cc_start: 0.7991 (ptp) cc_final: 0.7509 (ptp) REVERT: E 42 GLU cc_start: 0.7161 (tt0) cc_final: 0.6946 (tt0) REVERT: G 1 MET cc_start: 0.7979 (ptp) cc_final: 0.7747 (ptp) REVERT: G 43 THR cc_start: 0.8548 (m) cc_final: 0.8219 (p) REVERT: B 42 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7636 (tm-30) REVERT: D 26 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7171 (mmm160) REVERT: D 42 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7629 (tm-30) REVERT: F 26 ARG cc_start: 0.7477 (mmm160) cc_final: 0.7011 (mmm160) REVERT: F 42 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7907 (tm-30) REVERT: H 42 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7938 (tm-30) outliers start: 20 outliers final: 14 residues processed: 184 average time/residue: 0.2581 time to fit residues: 63.6450 Evaluate side-chains 175 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G 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 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 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.0060 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9784 Z= 0.178 Angle : 0.524 7.716 13336 Z= 0.275 Chirality : 0.039 0.153 1508 Planarity : 0.005 0.055 1676 Dihedral : 15.150 85.837 1840 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.60 % Allowed : 19.20 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.25), residues: 1160 helix: 1.39 (0.22), residues: 576 sheet: 0.24 (0.32), residues: 172 loop : -0.43 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.009 0.002 PHE E 137 TYR 0.019 0.002 TYR E 121 ARG 0.011 0.001 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 169 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 1.130 Fit side-chains REVERT: A 1 MET cc_start: 0.7452 (ptp) cc_final: 0.6977 (ptp) REVERT: A 17 ARG cc_start: 0.7717 (tmt170) cc_final: 0.7407 (tmm160) REVERT: C 1 MET cc_start: 0.7388 (ptp) cc_final: 0.6977 (ptp) REVERT: E 1 MET cc_start: 0.7693 (ptp) cc_final: 0.7292 (ptp) REVERT: G 1 MET cc_start: 0.7596 (ptp) cc_final: 0.7361 (ptp) REVERT: G 17 ARG cc_start: 0.7326 (ttm110) cc_final: 0.7123 (tmm160) REVERT: B 42 GLU cc_start: 0.7874 (tt0) cc_final: 0.7089 (tm-30) REVERT: D 26 ARG cc_start: 0.7421 (mmm160) cc_final: 0.7076 (mmm160) REVERT: D 42 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7637 (tm-30) REVERT: F 26 ARG cc_start: 0.7431 (mmm160) cc_final: 0.6987 (mmm160) REVERT: F 42 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7645 (tm-30) REVERT: H 26 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7283 (mmm160) REVERT: H 42 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 6 outliers final: 4 residues processed: 166 average time/residue: 0.2635 time to fit residues: 58.8366 Evaluate side-chains 162 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 H residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9784 Z= 0.195 Angle : 0.519 6.639 13336 Z= 0.271 Chirality : 0.039 0.151 1508 Planarity : 0.005 0.058 1676 Dihedral : 14.612 76.700 1840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.60 % Allowed : 19.60 % 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: 0.89 (0.25), residues: 1160 helix: 1.47 (0.22), residues: 584 sheet: 0.39 (0.32), residues: 172 loop : -0.54 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.014 0.002 PHE B 38 TYR 0.018 0.002 TYR E 121 ARG 0.017 0.000 ARG B 26 *********************** 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 fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 1.099 Fit side-chains REVERT: A 1 MET cc_start: 0.7479 (ptp) cc_final: 0.6912 (ptp) REVERT: C 1 MET cc_start: 0.7319 (ptp) cc_final: 0.6776 (ptp) REVERT: C 43 THR cc_start: 0.8261 (m) cc_final: 0.7866 (p) REVERT: E 17 ARG cc_start: 0.7351 (ttm110) cc_final: 0.7099 (tmm160) REVERT: E 25 ILE cc_start: 0.8949 (mt) cc_final: 0.8647 (mm) REVERT: G 1 MET cc_start: 0.7576 (ptp) cc_final: 0.7325 (ptp) REVERT: D 26 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7073 (mmm160) REVERT: D 42 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7437 (tm-30) REVERT: F 26 ARG cc_start: 0.7408 (mmm160) cc_final: 0.6955 (mmm160) REVERT: F 42 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7591 (tm-30) REVERT: H 26 ARG cc_start: 0.7524 (mmm160) cc_final: 0.7225 (mmm160) outliers start: 6 outliers final: 5 residues processed: 161 average time/residue: 0.2507 time to fit residues: 55.3139 Evaluate side-chains 158 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 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 64 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 0.0040 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9784 Z= 0.271 Angle : 0.552 6.701 13336 Z= 0.287 Chirality : 0.039 0.149 1508 Planarity : 0.005 0.052 1676 Dihedral : 14.404 80.011 1840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.60 % Allowed : 20.50 % Favored : 78.90 % 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: 1.43 (0.22), residues: 584 sheet: 0.31 (0.32), residues: 172 loop : -0.48 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.011 0.002 PHE C 124 TYR 0.018 0.002 TYR G 121 ARG 0.008 0.000 ARG A 87 *********************** 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 167 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.066 Fit side-chains REVERT: A 1 MET cc_start: 0.7605 (ptp) cc_final: 0.7195 (ptp) REVERT: A 17 ARG cc_start: 0.7634 (tmt170) cc_final: 0.7201 (ttp80) REVERT: C 17 ARG cc_start: 0.7685 (tmm160) cc_final: 0.7057 (ttm110) REVERT: E 17 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7128 (tmm160) REVERT: E 25 ILE cc_start: 0.8960 (mt) cc_final: 0.8679 (mm) REVERT: G 17 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7147 (ttm110) REVERT: G 25 ILE cc_start: 0.9011 (mt) cc_final: 0.8190 (mp) REVERT: D 26 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7118 (mmm160) REVERT: D 42 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7494 (tm-30) REVERT: F 26 ARG cc_start: 0.7434 (mmm160) cc_final: 0.6969 (mmm160) REVERT: F 42 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7637 (tm-30) REVERT: H 26 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7171 (mmm160) outliers start: 6 outliers final: 6 residues processed: 164 average time/residue: 0.2466 time to fit residues: 54.7785 Evaluate side-chains 163 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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 77 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 94 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9784 Z= 0.200 Angle : 0.535 7.148 13336 Z= 0.279 Chirality : 0.039 0.162 1508 Planarity : 0.004 0.051 1676 Dihedral : 13.847 88.213 1840 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.70 % Allowed : 20.40 % Favored : 78.90 % 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: 0.98 (0.25), residues: 1160 helix: 1.48 (0.22), residues: 584 sheet: 0.40 (0.32), residues: 188 loop : -0.40 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 2 PHE 0.008 0.001 PHE B 38 TYR 0.019 0.002 TYR E 121 ARG 0.009 0.000 ARG H 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 156 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 0.972 Fit side-chains REVERT: A 17 ARG cc_start: 0.7645 (tmt170) cc_final: 0.7405 (tmm160) REVERT: C 17 ARG cc_start: 0.7744 (tmm160) cc_final: 0.7048 (ttm110) REVERT: C 43 THR cc_start: 0.8162 (m) cc_final: 0.7830 (p) REVERT: E 25 ILE cc_start: 0.8959 (mt) cc_final: 0.8668 (mm) REVERT: G 1 MET cc_start: 0.7527 (ptp) cc_final: 0.7235 (ptp) REVERT: D 26 ARG cc_start: 0.7447 (mmm160) cc_final: 0.7093 (mmm160) REVERT: F 26 ARG cc_start: 0.7450 (mmm160) cc_final: 0.6995 (mmm160) REVERT: F 42 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7781 (tm-30) REVERT: H 26 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7174 (mmm160) REVERT: H 42 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 7 outliers final: 7 residues processed: 153 average time/residue: 0.2386 time to fit residues: 50.2345 Evaluate side-chains 155 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain E 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 77 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 64 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 overall best weight: 2.1602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9784 Z= 0.358 Angle : 0.602 6.916 13336 Z= 0.310 Chirality : 0.040 0.158 1508 Planarity : 0.005 0.052 1676 Dihedral : 14.110 88.910 1840 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.70 % Allowed : 20.70 % 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: 0.86 (0.25), residues: 1160 helix: 1.44 (0.22), residues: 576 sheet: 0.03 (0.31), residues: 192 loop : -0.35 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 2 PHE 0.015 0.002 PHE C 124 TYR 0.020 0.003 TYR G 121 ARG 0.008 0.001 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 161 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7577 (ptp) cc_final: 0.7264 (ptp) REVERT: A 17 ARG cc_start: 0.7699 (tmt170) cc_final: 0.7300 (ttp80) REVERT: E 17 ARG cc_start: 0.7656 (tmm160) cc_final: 0.7076 (ttm110) REVERT: G 1 MET cc_start: 0.7818 (ptp) cc_final: 0.7533 (ptp) REVERT: G 17 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6566 (ttm110) REVERT: D 26 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7123 (mmm160) REVERT: D 42 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7681 (tm-30) REVERT: F 42 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 26 ARG cc_start: 0.7579 (mmm160) cc_final: 0.7169 (mmm160) outliers start: 7 outliers final: 7 residues processed: 158 average time/residue: 0.2674 time to fit residues: 56.4858 Evaluate side-chains 158 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain E 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 77 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 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.195855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150614 restraints weight = 9352.599| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.94 r_work: 0.3420 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.177 Angle : 0.552 8.625 13336 Z= 0.288 Chirality : 0.039 0.173 1508 Planarity : 0.005 0.053 1676 Dihedral : 13.516 89.947 1840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: 1.03 (0.25), residues: 1160 helix: 1.45 (0.22), residues: 580 sheet: 0.56 (0.31), residues: 168 loop : -0.27 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 2 PHE 0.008 0.001 PHE B 38 TYR 0.020 0.003 TYR E 121 ARG 0.009 0.000 ARG B 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.39 seconds wall clock time: 42 minutes 28.82 seconds (2548.82 seconds total)