Starting phenix.real_space_refine on Sat Sep 12 18:52:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.map" model { file = "/net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xd0_33131/09_2026/7xd0_33131.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 14 5.16 5 C 7398 2.51 5 N 2466 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13222 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 811 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ARG K 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.45 residue: pdb=" N GLY K 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.25 residue: pdb=" N GLY K 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY K 76 " occ=0.25 Time building chain proxies: 2.65, per 1000 atoms: 0.20 Number of scatterers: 13222 At special positions: 0 Unit cell: (139.62, 136.398, 93.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 292 15.00 O 3052 8.00 N 2466 7.00 C 7398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 442.2 milliseconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 60.0% alpha, 6.1% beta 141 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.753A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.533A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.467A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.660A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.834A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.863A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.565A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.651A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.506A pdb=" N LYS L 27 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'K' and resid 22 through 35 removed outlier: 3.507A pdb=" N LYS K 27 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.530A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 96 through 98 removed outlier: 5.985A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.489A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.731A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.598A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 removed outlier: 3.598A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2876 1.33 - 1.45: 4188 1.45 - 1.57: 6370 1.57 - 1.69: 582 1.69 - 1.81: 26 Bond restraints: 14042 Sorted by residual: bond pdb=" C3' DG I 73 " pdb=" C2' DG I 73 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG I 13 " pdb=" C2' DG I 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 bond pdb=" C3' DT I 134 " pdb=" C2' DT I 134 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 ... (remaining 14037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18544 1.31 - 2.63: 1513 2.63 - 3.94: 127 3.94 - 5.26: 24 5.26 - 6.57: 5 Bond angle restraints: 20213 Sorted by residual: angle pdb=" N3 DT I 48 " pdb=" C4 DT I 48 " pdb=" O4 DT I 48 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 105 " pdb=" C4 DT I 105 " pdb=" O4 DT I 105 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 20208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 6275 34.47 - 68.93: 1416 68.93 - 103.40: 30 103.40 - 137.87: 0 137.87 - 172.33: 3 Dihedral angle restraints: 7724 sinusoidal: 5081 harmonic: 2643 Sorted by residual: dihedral pdb=" CA THR F 71 " pdb=" C THR F 71 " pdb=" N TYR F 72 " pdb=" CA TYR F 72 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ALA F 89 " pdb=" C ALA F 89 " pdb=" N LEU F 90 " pdb=" CA LEU F 90 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ALA F 69 " pdb=" C ALA F 69 " pdb=" N VAL F 70 " pdb=" CA VAL F 70 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1556 0.039 - 0.079: 543 0.079 - 0.118: 183 0.118 - 0.157: 26 0.157 - 0.197: 3 Chirality restraints: 2311 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB THR F 71 " pdb=" CA THR F 71 " pdb=" OG1 THR F 71 " pdb=" CG2 THR F 71 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2308 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LEU F 62 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 80 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.018 2.00e-02 2.50e+03 8.14e-03 1.82e+00 pdb=" N9 DA I 91 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.001 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 154 2.63 - 3.20: 10839 3.20 - 3.76: 23949 3.76 - 4.33: 31828 4.33 - 4.90: 45569 Nonbonded interactions: 112339 Sorted by model distance: nonbonded pdb=" CG ARG K 42 " pdb=" NH2 ARG K 72 " model vdw 2.062 3.520 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.132 3.040 nonbonded pdb=" O GLN L 62 " pdb=" OG SER L 65 " model vdw 2.132 3.040 nonbonded pdb=" O2 DC I 74 " pdb=" N2 DG J 74 " model vdw 2.183 2.496 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.223 3.040 ... (remaining 112334 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 37 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.005 0.039 14042 Z= 0.487 Angle : 0.732 6.573 20213 Z= 0.644 Chirality : 0.045 0.197 2311 Planarity : 0.003 0.046 1552 Dihedral : 27.036 172.333 6018 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.29), residues: 895 helix: 1.51 (0.23), residues: 562 sheet: -0.46 (0.79), residues: 50 loop : -0.06 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.018 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.49 (14042) covalent geometry : angle 0.73217 / 0.64 (20213) hydrogen bonds : bond 0.11505 / 7.42 ( 767) hydrogen bonds : angle 4.80620 / 3.63 ( 1915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.372 Fit side-chains REVERT: G 61 GLU cc_start: 0.7469 (tp30) cc_final: 0.7258 (tp30) REVERT: H 59 MET cc_start: 0.8586 (tpp) cc_final: 0.8375 (tpp) REVERT: H 116 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7607 (ttpp) REVERT: E 58 THR cc_start: 0.8782 (p) cc_final: 0.8522 (p) REVERT: D 68 ASP cc_start: 0.8486 (t0) cc_final: 0.8251 (t0) REVERT: L 74 ARG cc_start: -0.0092 (OUTLIER) cc_final: -0.0876 (mmm160) REVERT: K 1 MET cc_start: 0.0618 (tpt) cc_final: 0.0261 (tpt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1246 time to fit residues: 25.3808 Evaluate side-chains 124 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 108 ASN D 63 ASN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074949 restraints weight = 31761.093| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.62 r_work: 0.2862 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14042 Z= 0.184 Angle : 0.683 6.763 20213 Z= 0.393 Chirality : 0.049 0.428 2311 Planarity : 0.005 0.044 1552 Dihedral : 30.431 173.519 4206 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.78 % Allowed : 7.06 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.29), residues: 895 helix: 1.60 (0.22), residues: 571 sheet: -0.98 (0.72), residues: 50 loop : -0.00 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.018 0.002 TYR H 40 PHE 0.010 0.002 PHE F 61 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (14042) covalent geometry : angle 0.68343 / 0.39 (20213) hydrogen bonds : bond 0.05548 / 3.58 ( 767) hydrogen bonds : angle 3.78381 / 2.74 ( 1915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.406 Fit side-chains REVERT: F 25 ASN cc_start: 0.8430 (m-40) cc_final: 0.8118 (m-40) REVERT: G 61 GLU cc_start: 0.8223 (tp30) cc_final: 0.7888 (tp30) REVERT: H 54 ILE cc_start: 0.8620 (mm) cc_final: 0.8306 (tt) REVERT: E 58 THR cc_start: 0.8954 (p) cc_final: 0.8698 (p) REVERT: C 73 ASN cc_start: 0.7961 (t0) cc_final: 0.7742 (t0) REVERT: B 25 ASN cc_start: 0.8933 (m110) cc_final: 0.8423 (m-40) outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.1254 time to fit residues: 23.6742 Evaluate side-chains 122 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 38 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 125 GLN D 67 ASN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074358 restraints weight = 32143.478| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.40 r_work: 0.2848 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14042 Z= 0.148 Angle : 0.623 6.485 20213 Z= 0.365 Chirality : 0.046 0.406 2311 Planarity : 0.004 0.044 1552 Dihedral : 30.516 175.060 4202 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.57 % Allowed : 7.58 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 895 helix: 1.84 (0.23), residues: 571 sheet: -0.95 (0.72), residues: 50 loop : 0.08 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 92 TYR 0.019 0.002 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14042) covalent geometry : angle 0.62254 / 0.37 (20213) hydrogen bonds : bond 0.04898 / 3.16 ( 767) hydrogen bonds : angle 3.51980 / 2.56 ( 1915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.362 Fit side-chains REVERT: F 25 ASN cc_start: 0.8382 (m-40) cc_final: 0.8107 (m-40) REVERT: G 61 GLU cc_start: 0.8190 (tp30) cc_final: 0.7902 (tp30) REVERT: H 54 ILE cc_start: 0.8552 (mm) cc_final: 0.8337 (tt) REVERT: E 58 THR cc_start: 0.8957 (p) cc_final: 0.8708 (p) REVERT: C 73 ASN cc_start: 0.8098 (t0) cc_final: 0.7840 (t0) REVERT: B 25 ASN cc_start: 0.8907 (m-40) cc_final: 0.8287 (m-40) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.1161 time to fit residues: 22.0231 Evaluate side-chains 123 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 84 ASN A 125 GLN D 63 ASN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073134 restraints weight = 32031.284| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.53 r_work: 0.2834 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14042 Z= 0.165 Angle : 0.640 6.769 20213 Z= 0.368 Chirality : 0.046 0.417 2311 Planarity : 0.004 0.045 1552 Dihedral : 30.609 175.705 4202 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.83 % Allowed : 9.41 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.29), residues: 895 helix: 1.88 (0.22), residues: 571 sheet: -0.90 (0.73), residues: 50 loop : -0.01 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.017 0.002 TYR H 40 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (14042) covalent geometry : angle 0.63960 / 0.37 (20213) hydrogen bonds : bond 0.04941 / 3.19 ( 767) hydrogen bonds : angle 3.39830 / 2.47 ( 1915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.374 Fit side-chains REVERT: F 25 ASN cc_start: 0.8341 (m-40) cc_final: 0.8064 (m-40) REVERT: G 61 GLU cc_start: 0.8258 (tp30) cc_final: 0.7956 (tp30) REVERT: H 54 ILE cc_start: 0.8598 (mm) cc_final: 0.8385 (tt) REVERT: E 58 THR cc_start: 0.8958 (p) cc_final: 0.8709 (p) REVERT: C 73 ASN cc_start: 0.8099 (t0) cc_final: 0.7876 (t0) REVERT: B 25 ASN cc_start: 0.8913 (m-40) cc_final: 0.8161 (m110) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.1235 time to fit residues: 23.1213 Evaluate side-chains 127 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 38 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 125 GLN D 63 ASN C 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074510 restraints weight = 32061.998| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.48 r_work: 0.2857 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14042 Z= 0.132 Angle : 0.607 6.636 20213 Z= 0.355 Chirality : 0.045 0.403 2311 Planarity : 0.003 0.044 1552 Dihedral : 30.562 176.371 4202 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.44 % Allowed : 10.72 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.29), residues: 895 helix: 2.07 (0.23), residues: 570 sheet: -0.97 (0.71), residues: 52 loop : 0.02 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.016 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (14042) covalent geometry : angle 0.60742 / 0.35 (20213) hydrogen bonds : bond 0.04607 / 2.97 ( 767) hydrogen bonds : angle 3.24123 / 2.35 ( 1915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.364 Fit side-chains REVERT: G 61 GLU cc_start: 0.8119 (tp30) cc_final: 0.7898 (tp30) REVERT: H 54 ILE cc_start: 0.8535 (mm) cc_final: 0.8335 (tt) REVERT: E 58 THR cc_start: 0.8949 (p) cc_final: 0.8704 (p) REVERT: D 59 MET cc_start: 0.8915 (tpp) cc_final: 0.8472 (tpp) REVERT: C 73 ASN cc_start: 0.8147 (t0) cc_final: 0.7914 (t0) REVERT: B 25 ASN cc_start: 0.8844 (m-40) cc_final: 0.8110 (m110) outliers start: 11 outliers final: 7 residues processed: 141 average time/residue: 0.1264 time to fit residues: 25.7094 Evaluate side-chains 129 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 125 GLN D 63 ASN D 67 ASN C 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069944 restraints weight = 31856.877| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.76 r_work: 0.2843 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14042 Z= 0.175 Angle : 0.645 6.968 20213 Z= 0.368 Chirality : 0.046 0.421 2311 Planarity : 0.004 0.045 1552 Dihedral : 30.689 176.511 4202 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.35 % Allowed : 10.20 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.29), residues: 895 helix: 1.96 (0.22), residues: 571 sheet: -0.90 (0.72), residues: 52 loop : -0.09 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.023 0.002 TYR D 40 PHE 0.012 0.002 PHE F 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (14042) covalent geometry : angle 0.64523 / 0.37 (20213) hydrogen bonds : bond 0.04932 / 3.19 ( 767) hydrogen bonds : angle 3.26546 / 2.36 ( 1915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.300 Fit side-chains REVERT: F 84 MET cc_start: 0.8466 (mmt) cc_final: 0.8150 (mmm) REVERT: G 61 GLU cc_start: 0.8167 (tp30) cc_final: 0.7882 (tp30) REVERT: H 83 TYR cc_start: 0.7780 (m-10) cc_final: 0.7570 (m-10) REVERT: E 58 THR cc_start: 0.8887 (p) cc_final: 0.8633 (p) REVERT: E 73 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8543 (pp20) REVERT: C 73 ASN cc_start: 0.8089 (t0) cc_final: 0.7867 (t0) REVERT: C 101 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8960 (p) REVERT: B 25 ASN cc_start: 0.8818 (m-40) cc_final: 0.8182 (m110) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.1226 time to fit residues: 23.1611 Evaluate side-chains 129 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN A 125 GLN D 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069315 restraints weight = 31850.466| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.10 r_work: 0.2829 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14042 Z= 0.196 Angle : 0.672 7.332 20213 Z= 0.379 Chirality : 0.048 0.429 2311 Planarity : 0.004 0.046 1552 Dihedral : 30.800 176.935 4202 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.75 % Allowed : 9.80 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.29), residues: 895 helix: 1.89 (0.23), residues: 571 sheet: -0.87 (0.73), residues: 52 loop : -0.19 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.020 0.002 TYR D 40 PHE 0.014 0.002 PHE F 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (14042) covalent geometry : angle 0.67181 / 0.38 (20213) hydrogen bonds : bond 0.05112 / 3.32 ( 767) hydrogen bonds : angle 3.29070 / 2.39 ( 1915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.319 Fit side-chains REVERT: G 61 GLU cc_start: 0.8094 (tp30) cc_final: 0.7867 (tp30) REVERT: E 73 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8492 (pp20) REVERT: D 59 MET cc_start: 0.8969 (tpp) cc_final: 0.8555 (tpp) REVERT: C 38 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6923 (t0) REVERT: C 73 ASN cc_start: 0.8112 (t0) cc_final: 0.7911 (t0) REVERT: C 101 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8963 (p) REVERT: B 25 ASN cc_start: 0.8826 (m-40) cc_final: 0.8133 (m-40) outliers start: 21 outliers final: 14 residues processed: 127 average time/residue: 0.1212 time to fit residues: 22.2410 Evaluate side-chains 132 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.0010 chunk 83 optimal weight: 10.0000 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 125 GLN D 63 ASN C 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073978 restraints weight = 31528.385| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.22 r_work: 0.2860 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14042 Z= 0.135 Angle : 0.618 8.372 20213 Z= 0.357 Chirality : 0.045 0.407 2311 Planarity : 0.004 0.045 1552 Dihedral : 30.696 177.222 4202 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.35 % Allowed : 10.85 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.29), residues: 895 helix: 2.07 (0.23), residues: 571 sheet: -0.75 (0.73), residues: 52 loop : -0.09 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.019 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (14042) covalent geometry : angle 0.61846 / 0.36 (20213) hydrogen bonds : bond 0.04594 / 2.96 ( 767) hydrogen bonds : angle 3.15685 / 2.29 ( 1915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.385 Fit side-chains REVERT: G 61 GLU cc_start: 0.8095 (tp30) cc_final: 0.7886 (tp30) REVERT: E 58 THR cc_start: 0.8943 (p) cc_final: 0.8692 (p) REVERT: E 73 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8456 (pp20) REVERT: D 59 MET cc_start: 0.8973 (tpp) cc_final: 0.8524 (tpp) REVERT: C 101 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 25 ASN cc_start: 0.8744 (m-40) cc_final: 0.8184 (m110) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.1200 time to fit residues: 22.6481 Evaluate side-chains 130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 0.0010 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN A 125 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074799 restraints weight = 31970.181| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.36 r_work: 0.2863 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14042 Z= 0.124 Angle : 0.603 8.217 20213 Z= 0.351 Chirality : 0.044 0.399 2311 Planarity : 0.003 0.046 1552 Dihedral : 30.630 178.254 4202 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.44 % Allowed : 11.63 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.29), residues: 895 helix: 2.19 (0.23), residues: 568 sheet: -0.69 (0.72), residues: 52 loop : -0.11 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 35 TYR 0.020 0.001 TYR H 40 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 (14042) covalent geometry : angle 0.60338 / 0.35 (20213) hydrogen bonds : bond 0.04425 / 2.84 ( 767) hydrogen bonds : angle 3.09566 / 2.24 ( 1915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.352 Fit side-chains REVERT: G 61 GLU cc_start: 0.8149 (tp30) cc_final: 0.7944 (tp30) REVERT: E 58 THR cc_start: 0.8934 (p) cc_final: 0.8683 (p) REVERT: E 73 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8505 (pp20) REVERT: C 101 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8949 (p) REVERT: B 25 ASN cc_start: 0.8758 (m-40) cc_final: 0.8102 (m110) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.1230 time to fit residues: 23.1135 Evaluate side-chains 129 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 113 optimal weight: 0.0470 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN H 84 ASN A 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077010 restraints weight = 32006.587| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.13 r_work: 0.2903 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14042 Z= 0.123 Angle : 0.595 8.519 20213 Z= 0.346 Chirality : 0.043 0.397 2311 Planarity : 0.003 0.047 1552 Dihedral : 30.593 179.049 4202 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.57 % Allowed : 12.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.29), residues: 895 helix: 2.22 (0.22), residues: 568 sheet: -0.52 (0.72), residues: 52 loop : -0.07 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.018 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.12 (14042) covalent geometry : angle 0.59519 / 0.35 (20213) hydrogen bonds : bond 0.04360 / 2.79 ( 767) hydrogen bonds : angle 3.03495 / 2.19 ( 1915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.350 Fit side-chains REVERT: H 80 LEU cc_start: 0.9208 (tp) cc_final: 0.8936 (tp) REVERT: E 58 THR cc_start: 0.8898 (p) cc_final: 0.8645 (p) REVERT: E 73 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8417 (pp20) REVERT: E 76 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7711 (pt0) REVERT: C 101 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8967 (p) REVERT: B 25 ASN cc_start: 0.8704 (m-40) cc_final: 0.8121 (m-40) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.1207 time to fit residues: 22.6415 Evaluate side-chains 127 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.0070 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 105 optimal weight: 0.0000 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071996 restraints weight = 31795.635| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.76 r_work: 0.2885 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (14 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14042 Z= 0.136 Angle : 0.612 10.226 20213 Z= 0.351 Chirality : 0.044 0.404 2311 Planarity : 0.004 0.047 1552 Dihedral : 30.632 178.769 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.44 % Allowed : 12.42 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.29), residues: 895 helix: 2.27 (0.22), residues: 568 sheet: -0.36 (0.72), residues: 52 loop : -0.11 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 86 TYR 0.023 0.002 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (14042) covalent geometry : angle 0.61196 / 0.35 (20213) hydrogen bonds : bond 0.04482 / 2.88 ( 767) hydrogen bonds : angle 3.05402 / 2.21 ( 1915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.00 seconds wall clock time: 55 minutes 27.59 seconds (3327.59 seconds total)