Starting phenix.real_space_refine on Thu Jul 31 12:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.map" model { file = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2025/7ea5_31039.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 7743 2.51 5 N 2547 2.21 5 O 3154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13770 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1866 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 12395 SG CYS K 97 60.815 66.338 50.205 1.00 41.97 S ATOM 12450 SG CYS K 105 64.400 68.875 51.580 1.00 57.96 S ATOM 12168 SG CYS K 68 65.754 65.298 51.958 1.00 49.16 S ATOM 12182 SG CYS K 70 68.099 67.624 50.381 1.00 61.08 S ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 13648 SG CYS K 248 53.165 52.723 14.294 1.00 68.97 S ATOM 13705 SG CYS K 255 56.658 49.593 12.841 1.00 58.18 S Time building chain proxies: 7.92, per 1000 atoms: 0.58 Number of scatterers: 13770 At special positions: 0 Unit cell: (154.78, 91.56, 130.8, 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 3 29.99 S 33 16.00 P 290 15.00 O 3154 8.00 N 2547 7.00 C 7743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 97 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 70 " pdb=" ZN K 303 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 255 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 248 " 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 59.0% alpha, 3.9% beta 143 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.522A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.668A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.500A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.534A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.755A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.922A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.584A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.563A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.696A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.830A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.191A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.753A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.580A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.352A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.721A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 36 through 46 removed outlier: 3.598A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.764A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.761A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 44 removed outlier: 3.908A pdb=" N GLU K 38 " --> pdb=" O PRO K 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 42 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 156 through 169 removed outlier: 4.152A pdb=" N ASP K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 196 removed outlier: 3.987A pdb=" N ARG K 195 " --> pdb=" O SER K 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE K 196 " --> pdb=" O LEU K 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 192 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.193A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.179A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.627A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.986A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.130A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.550A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.203A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 45 through 46 removed outlier: 6.334A pdb=" N GLU K 45 " --> pdb=" O GLY K 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 122 through 124 removed outlier: 4.030A pdb=" N ALA K 123 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 152 through 155 Processing sheet with id=AB5, first strand: chain 'K' and resid 210 through 211 405 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 4521 1.46 - 1.58: 6418 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 14610 Sorted by residual: bond pdb=" C2 SAM K 304 " pdb=" N3 SAM K 304 " ideal model delta sigma weight residual 1.322 1.382 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C8 SAM K 304 " pdb=" N7 SAM K 304 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C2 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C6 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.337 1.379 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 20317 1.73 - 3.45: 588 3.45 - 5.18: 45 5.18 - 6.90: 11 6.90 - 8.63: 6 Bond angle restraints: 20967 Sorted by residual: angle pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sigma weight residual 120.20 124.75 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N SER D 84 " pdb=" CA SER D 84 " pdb=" C SER D 84 " ideal model delta sigma weight residual 114.56 110.74 3.82 1.27e+00 6.20e-01 9.07e+00 angle pdb=" C GLY C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta sigma weight residual 119.78 123.45 -3.67 1.24e+00 6.50e-01 8.74e+00 angle pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.28e+00 angle pdb=" O SAM K 304 " pdb=" C SAM K 304 " pdb=" OXT SAM K 304 " ideal model delta sigma weight residual 126.77 118.14 8.63 3.00e+00 1.11e-01 8.28e+00 ... (remaining 20962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6773 35.35 - 70.70: 1261 70.70 - 106.05: 16 106.05 - 141.41: 3 141.41 - 176.76: 1 Dihedral angle restraints: 8054 sinusoidal: 5214 harmonic: 2840 Sorted by residual: dihedral pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sinusoidal sigma weight residual -140.00 36.76 -176.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1846 0.044 - 0.089: 398 0.089 - 0.133: 97 0.133 - 0.177: 14 0.177 - 0.222: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" SD SAM K 304 " pdb=" CG SAM K 304 " pdb=" CE SAM K 304 " pdb=" C5' SAM K 304 " both_signs ideal model delta sigma weight residual False 5.50 5.28 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' SAM K 304 " pdb=" C2' SAM K 304 " pdb=" N9 SAM K 304 " pdb=" O4' SAM K 304 " both_signs ideal model delta sigma weight residual False 2.30 2.48 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM K 304 " pdb=" C1' SAM K 304 " pdb=" C3' SAM K 304 " pdb=" O2' SAM K 304 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2355 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 252 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO K 253 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO G 80 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.027 5.00e-02 4.00e+02 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3573 2.84 - 3.35: 10795 3.35 - 3.87: 25371 3.87 - 4.38: 28991 4.38 - 4.90: 42183 Nonbonded interactions: 110913 Sorted by model distance: nonbonded pdb=" O ILE K 89 " pdb=" OG1 THR K 93 " model vdw 2.319 3.040 nonbonded pdb=" O CYS K 197 " pdb=" OH TYR K 236 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 104 " model vdw 2.339 3.040 nonbonded pdb=" NH1 ARG C 42 " pdb=" OG1 THR D 85 " model vdw 2.377 3.120 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.402 3.120 ... (remaining 110908 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 40.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.011 0.588 14620 Z= 0.396 Angle : 0.682 8.630 20967 Z= 0.410 Chirality : 0.041 0.222 2358 Planarity : 0.005 0.059 1663 Dihedral : 24.985 176.756 6222 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.00 (0.21), residues: 957 helix: -1.43 (0.17), residues: 568 sheet: -2.01 (1.11), residues: 28 loop : -2.78 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP K 210 HIS 0.005 0.001 HIS F 75 PHE 0.019 0.002 PHE G 25 TYR 0.013 0.001 TYR F 98 ARG 0.004 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.10338 ( 772) hydrogen bonds : angle 4.42462 ( 1934) metal coordination : bond 0.44504 ( 8) covalent geometry : bond 0.00373 (14610) covalent geometry : angle 0.68180 (20967) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8625 (mttt) cc_final: 0.8311 (mtpp) REVERT: C 101 THR cc_start: 0.8310 (m) cc_final: 0.8042 (m) REVERT: F 31 LYS cc_start: 0.8787 (tttt) cc_final: 0.8463 (tttm) REVERT: K 85 ASP cc_start: 0.6343 (m-30) cc_final: 0.6074 (t0) REVERT: K 233 THR cc_start: 0.6394 (p) cc_final: 0.6042 (p) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4286 time to fit residues: 151.5567 Evaluate side-chains 159 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 68 ASN D 106 HIS E 39 HIS E 68 GLN F 25 ASN G 38 ASN G 84 GLN K 112 GLN K 115 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127211 restraints weight = 17368.691| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.22 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14620 Z= 0.214 Angle : 0.588 6.799 20967 Z= 0.342 Chirality : 0.037 0.149 2358 Planarity : 0.005 0.042 1663 Dihedral : 29.426 179.095 4280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.69 % Allowed : 7.51 % Favored : 90.80 % 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: -0.81 (0.26), residues: 957 helix: 0.71 (0.21), residues: 571 sheet: -1.50 (1.16), residues: 28 loop : -2.60 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP K 210 HIS 0.006 0.002 HIS G 31 PHE 0.024 0.002 PHE G 25 TYR 0.017 0.002 TYR G 50 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 772) hydrogen bonds : angle 2.86717 ( 1934) metal coordination : bond 0.00627 ( 8) covalent geometry : bond 0.00499 (14610) covalent geometry : angle 0.58833 (20967) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.9085 (p) cc_final: 0.8842 (t) REVERT: B 24 ASP cc_start: 0.6956 (p0) cc_final: 0.6746 (p0) REVERT: B 79 LYS cc_start: 0.8511 (mttt) cc_final: 0.8301 (mtpp) REVERT: C 89 ASN cc_start: 0.8783 (m-40) cc_final: 0.8577 (m110) REVERT: D 61 SER cc_start: 0.8909 (t) cc_final: 0.8675 (m) REVERT: E 39 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7294 (t-170) REVERT: E 115 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8361 (mtmm) REVERT: F 68 ASP cc_start: 0.8011 (m-30) cc_final: 0.7778 (m-30) REVERT: G 36 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7838 (tttp) REVERT: K 85 ASP cc_start: 0.6527 (m-30) cc_final: 0.6244 (t0) REVERT: K 241 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.4967 (p90) outliers start: 14 outliers final: 8 residues processed: 185 average time/residue: 0.3563 time to fit residues: 86.6479 Evaluate side-chains 167 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.180954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133060 restraints weight = 17509.856| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.50 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14620 Z= 0.137 Angle : 0.511 6.505 20967 Z= 0.305 Chirality : 0.033 0.149 2358 Planarity : 0.004 0.039 1663 Dihedral : 29.297 177.526 4280 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.09 % Allowed : 11.02 % Favored : 87.89 % 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: 0.29 (0.27), residues: 957 helix: 1.71 (0.22), residues: 569 sheet: -1.14 (1.20), residues: 28 loop : -2.33 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 210 HIS 0.014 0.001 HIS E 39 PHE 0.012 0.001 PHE K 159 TYR 0.008 0.001 TYR K 147 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 772) hydrogen bonds : angle 2.57304 ( 1934) metal coordination : bond 0.00217 ( 8) covalent geometry : bond 0.00293 (14610) covalent geometry : angle 0.51083 (20967) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.059 Fit side-chains REVERT: C 89 ASN cc_start: 0.8626 (m-40) cc_final: 0.8378 (m110) REVERT: D 76 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: G 113 SER cc_start: 0.9082 (m) cc_final: 0.8807 (p) REVERT: K 85 ASP cc_start: 0.6562 (m-30) cc_final: 0.6136 (t0) REVERT: K 233 THR cc_start: 0.6515 (p) cc_final: 0.6241 (m) REVERT: K 241 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.4594 (p90) outliers start: 9 outliers final: 8 residues processed: 158 average time/residue: 0.3476 time to fit residues: 73.4190 Evaluate side-chains 153 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129271 restraints weight = 17296.102| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.56 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14620 Z= 0.162 Angle : 0.529 6.218 20967 Z= 0.313 Chirality : 0.034 0.144 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.363 178.281 4280 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.06 % Allowed : 10.90 % Favored : 87.05 % 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: 0.59 (0.28), residues: 957 helix: 1.92 (0.22), residues: 571 sheet: -0.98 (1.22), residues: 28 loop : -2.17 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 210 HIS 0.005 0.001 HIS E 39 PHE 0.018 0.002 PHE K 159 TYR 0.010 0.001 TYR F 51 ARG 0.009 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 772) hydrogen bonds : angle 2.58890 ( 1934) metal coordination : bond 0.00102 ( 8) covalent geometry : bond 0.00362 (14610) covalent geometry : angle 0.52939 (20967) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8734 (m-40) cc_final: 0.8435 (m110) REVERT: D 56 MET cc_start: 0.8138 (tpp) cc_final: 0.7851 (mmm) REVERT: D 76 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7729 (mtm-85) REVERT: E 39 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7444 (t-170) REVERT: F 59 LYS cc_start: 0.8253 (tttt) cc_final: 0.8045 (tttp) REVERT: K 233 THR cc_start: 0.6590 (p) cc_final: 0.6319 (m) REVERT: K 241 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.4684 (p90) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.3604 time to fit residues: 78.2968 Evaluate side-chains 159 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 31 HIS F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121465 restraints weight = 17384.651| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.74 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14620 Z= 0.309 Angle : 0.665 8.339 20967 Z= 0.380 Chirality : 0.041 0.154 2358 Planarity : 0.006 0.051 1663 Dihedral : 29.765 178.854 4280 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.27 % Allowed : 11.26 % Favored : 85.47 % 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: 0.02 (0.27), residues: 957 helix: 1.33 (0.22), residues: 572 sheet: -1.35 (1.16), residues: 28 loop : -2.16 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 210 HIS 0.015 0.002 HIS E 39 PHE 0.034 0.003 PHE G 25 TYR 0.015 0.002 TYR F 51 ARG 0.009 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.07305 ( 772) hydrogen bonds : angle 2.96940 ( 1934) metal coordination : bond 0.00328 ( 8) covalent geometry : bond 0.00737 (14610) covalent geometry : angle 0.66517 (20967) Misc. bond : bond 0.00177 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.012 Fit side-chains REVERT: A 131 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: D 56 MET cc_start: 0.8482 (tpp) cc_final: 0.8242 (tpt) REVERT: D 105 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8145 (tttp) REVERT: E 115 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: G 75 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8366 (mmtp) REVERT: H 90 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7696 (mp0) REVERT: K 241 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5776 (p90) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.3516 time to fit residues: 74.4654 Evaluate side-chains 160 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN K 90 ASN K 112 GLN K 115 GLN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128769 restraints weight = 17530.443| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.33 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14620 Z= 0.136 Angle : 0.516 6.361 20967 Z= 0.309 Chirality : 0.033 0.154 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.280 176.232 4280 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.18 % Allowed : 12.95 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 957 helix: 2.08 (0.22), residues: 569 sheet: -0.67 (1.07), residues: 28 loop : -2.01 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 210 HIS 0.002 0.000 HIS F 75 PHE 0.026 0.001 PHE K 159 TYR 0.007 0.001 TYR K 241 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 772) hydrogen bonds : angle 2.49453 ( 1934) metal coordination : bond 0.00075 ( 8) covalent geometry : bond 0.00284 (14610) covalent geometry : angle 0.51594 (20967) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8426 (tptt) cc_final: 0.8127 (tptm) REVERT: C 89 ASN cc_start: 0.8723 (m-40) cc_final: 0.8438 (m110) REVERT: D 56 MET cc_start: 0.8066 (tpp) cc_final: 0.7858 (mmm) REVERT: G 75 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8328 (mmtp) REVERT: H 56 MET cc_start: 0.7692 (tpp) cc_final: 0.7377 (mmm) REVERT: H 76 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7750 (ttm170) REVERT: K 241 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5001 (p90) outliers start: 18 outliers final: 11 residues processed: 164 average time/residue: 0.4709 time to fit residues: 103.3746 Evaluate side-chains 154 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128600 restraints weight = 17516.846| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.36 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14620 Z= 0.138 Angle : 0.516 6.456 20967 Z= 0.308 Chirality : 0.033 0.149 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.195 177.735 4280 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.06 % Allowed : 13.20 % Favored : 84.75 % 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: 1.18 (0.28), residues: 957 helix: 2.35 (0.22), residues: 569 sheet: -0.25 (1.14), residues: 28 loop : -1.88 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 210 HIS 0.002 0.001 HIS G 31 PHE 0.030 0.001 PHE K 159 TYR 0.012 0.001 TYR K 236 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 772) hydrogen bonds : angle 2.45681 ( 1934) metal coordination : bond 0.00126 ( 8) covalent geometry : bond 0.00296 (14610) covalent geometry : angle 0.51612 (20967) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8706 (m-40) cc_final: 0.8414 (m110) REVERT: G 75 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8325 (mmtp) REVERT: H 43 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8080 (mmtm) REVERT: H 56 MET cc_start: 0.7727 (tpp) cc_final: 0.7114 (tpt) REVERT: H 76 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7781 (ttm170) REVERT: H 90 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: K 241 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5092 (p90) outliers start: 17 outliers final: 10 residues processed: 153 average time/residue: 0.3722 time to fit residues: 76.1336 Evaluate side-chains 154 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 0.0470 chunk 74 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126554 restraints weight = 17359.927| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.36 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14620 Z= 0.167 Angle : 0.546 7.089 20967 Z= 0.321 Chirality : 0.034 0.143 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.242 178.169 4280 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.69 % Allowed : 14.16 % Favored : 84.14 % 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: 1.09 (0.28), residues: 957 helix: 2.25 (0.22), residues: 572 sheet: -0.19 (1.13), residues: 28 loop : -1.89 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS G 31 PHE 0.039 0.002 PHE K 159 TYR 0.012 0.001 TYR K 236 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 772) hydrogen bonds : angle 2.55798 ( 1934) metal coordination : bond 0.00104 ( 8) covalent geometry : bond 0.00378 (14610) covalent geometry : angle 0.54557 (20967) Misc. bond : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8640 (m-40) cc_final: 0.8329 (m110) REVERT: G 75 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8337 (mmtp) REVERT: H 90 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: K 213 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7759 (mtmm) REVERT: K 241 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5235 (p90) outliers start: 14 outliers final: 12 residues processed: 149 average time/residue: 0.4354 time to fit residues: 89.6001 Evaluate side-chains 155 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128000 restraints weight = 17221.516| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.34 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14620 Z= 0.141 Angle : 0.528 8.256 20967 Z= 0.313 Chirality : 0.033 0.143 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.171 177.567 4280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.69 % Allowed : 14.04 % Favored : 84.26 % 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: 1.29 (0.28), residues: 957 helix: 2.43 (0.22), residues: 567 sheet: -0.11 (1.14), residues: 28 loop : -1.79 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 210 HIS 0.002 0.001 HIS G 31 PHE 0.041 0.001 PHE K 159 TYR 0.009 0.001 TYR K 236 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 772) hydrogen bonds : angle 2.48709 ( 1934) metal coordination : bond 0.00130 ( 8) covalent geometry : bond 0.00304 (14610) covalent geometry : angle 0.52757 (20967) Misc. bond : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8701 (m-40) cc_final: 0.8465 (m110) REVERT: G 75 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8310 (mmtp) REVERT: H 43 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8063 (mmtm) REVERT: H 56 MET cc_start: 0.7970 (tpt) cc_final: 0.7662 (mmm) REVERT: H 90 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: K 241 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.5197 (p90) outliers start: 14 outliers final: 11 residues processed: 148 average time/residue: 0.4772 time to fit residues: 94.6495 Evaluate side-chains 153 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 112 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.176913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126712 restraints weight = 17248.014| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.32 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14620 Z= 0.165 Angle : 0.545 7.922 20967 Z= 0.320 Chirality : 0.034 0.135 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.212 178.206 4280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.69 % Allowed : 14.53 % Favored : 83.78 % 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: 1.17 (0.28), residues: 957 helix: 2.29 (0.22), residues: 568 sheet: -0.15 (1.15), residues: 28 loop : -1.77 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS G 31 PHE 0.042 0.002 PHE K 159 TYR 0.012 0.001 TYR K 236 ARG 0.010 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 772) hydrogen bonds : angle 2.54623 ( 1934) metal coordination : bond 0.00084 ( 8) covalent geometry : bond 0.00372 (14610) covalent geometry : angle 0.54450 (20967) Misc. bond : bond 0.00115 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8575 (tptm) cc_final: 0.8295 (tttt) REVERT: C 89 ASN cc_start: 0.8707 (m-40) cc_final: 0.8402 (m110) REVERT: H 56 MET cc_start: 0.8015 (tpt) cc_final: 0.7449 (tpt) REVERT: H 90 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: K 241 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.5251 (p90) outliers start: 14 outliers final: 12 residues processed: 147 average time/residue: 0.5845 time to fit residues: 114.3725 Evaluate side-chains 152 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 218 MET Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125964 restraints weight = 17373.969| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.30 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14620 Z= 0.168 Angle : 0.547 7.990 20967 Z= 0.321 Chirality : 0.034 0.136 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.222 178.045 4280 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.94 % Allowed : 14.65 % Favored : 83.41 % 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: 1.14 (0.28), residues: 957 helix: 2.23 (0.22), residues: 568 sheet: -0.11 (1.16), residues: 28 loop : -1.73 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS G 31 PHE 0.036 0.002 PHE K 159 TYR 0.009 0.001 TYR K 236 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 772) hydrogen bonds : angle 2.56018 ( 1934) metal coordination : bond 0.00099 ( 8) covalent geometry : bond 0.00381 (14610) covalent geometry : angle 0.54733 (20967) Misc. bond : bond 0.00121 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6005.79 seconds wall clock time: 112 minutes 22.53 seconds (6742.53 seconds total)