Starting phenix.real_space_refine on Sun Mar 17 02:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/03_2024/8jhf_36264_updated.pdb" } resolution = 3.68 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= 0.003 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 1772 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 320 5.49 5 S 35 5.16 5 C 8219 2.51 5 N 2739 2.21 5 O 3389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 225": "OE1" <-> "OE2" Residue "K GLU 247": "OE1" <-> "OE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3253 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3307 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1726 SG CYS K 319 83.531 34.352 85.709 1.00145.38 S ATOM 1741 SG CYS K 321 84.756 36.893 84.198 1.00141.85 S ATOM 1766 SG CYS K 324 86.241 36.603 85.599 1.00143.31 S Time building chain proxies: 8.22, per 1000 atoms: 0.56 Number of scatterers: 14703 At special positions: 0 Unit cell: (110.4, 125.12, 142.6, 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 1 29.99 S 35 16.00 P 320 15.00 O 3389 8.00 N 2739 7.00 C 8219 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 - 3.50 Amino acid : False - 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: 7.41 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 2 sheets defined 52.7% alpha, 1.4% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 7.87 Creating SS restraints... Processing helix chain 'K' and resid 78 through 93 removed outlier: 3.560A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 150 through 158 Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 175 through 190 removed outlier: 3.689A pdb=" N PHE K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'K' and resid 322 through 326 Processing helix chain 'K' and resid 355 through 359 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 112 removed outlier: 4.037A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.109A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 50 through 70 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 54 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.653A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.053A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.878A pdb=" N SER G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 75 Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'G' and resid 115 through 118 No H-bonds generated for 'chain 'G' and resid 115 through 118' Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 54 through 80 Processing helix chain 'H' and resid 88 through 97 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.563A pdb=" N THR H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 229 through 234 removed outlier: 4.324A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 280 through 282 364 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3082 1.33 - 1.45: 4823 1.45 - 1.57: 7022 1.57 - 1.69: 638 1.69 - 1.81: 55 Bond restraints: 15620 Sorted by residual: bond pdb=" N ASP G 93 " pdb=" CA ASP G 93 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.17e+00 bond pdb=" C2 SAM K 402 " pdb=" N3 SAM K 402 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" N ASN K 221 " pdb=" CA ASN K 221 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.37e+00 bond pdb=" N LYS K 219 " pdb=" CA LYS K 219 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.41e-02 5.03e+03 8.14e+00 bond pdb=" N GLU K 233 " pdb=" CA GLU K 233 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.11e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.51: 1495 105.51 - 112.61: 8701 112.61 - 119.71: 5053 119.71 - 126.82: 6270 126.82 - 133.92: 925 Bond angle restraints: 22444 Sorted by residual: angle pdb=" N LEU G 96 " pdb=" CA LEU G 96 " pdb=" C LEU G 96 " ideal model delta sigma weight residual 111.82 106.63 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" C LEU G 99 " pdb=" N ILE G 100 " pdb=" CA ILE G 100 " ideal model delta sigma weight residual 121.80 115.96 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA LEU D 98 " pdb=" CB LEU D 98 " pdb=" CG LEU D 98 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.06e+01 angle pdb=" O SAM K 402 " pdb=" C SAM K 402 " pdb=" OXT SAM K 402 " ideal model delta sigma weight residual 126.77 117.79 8.98 3.00e+00 1.11e-01 8.97e+00 angle pdb=" CA GLU G 95 " pdb=" C GLU G 95 " pdb=" O GLU G 95 " ideal model delta sigma weight residual 120.82 117.69 3.13 1.05e+00 9.07e-01 8.91e+00 ... (remaining 22439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 7087 35.97 - 71.94: 1452 71.94 - 107.90: 24 107.90 - 143.87: 1 143.87 - 179.84: 5 Dihedral angle restraints: 8569 sinusoidal: 5598 harmonic: 2971 Sorted by residual: dihedral pdb=" C4' DT J 138 " pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " pdb=" P DC J 139 " ideal model delta sinusoidal sigma weight residual -140.00 39.84 -179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 145 " pdb=" C3' DA I 145 " pdb=" O3' DA I 145 " pdb=" P DT I 146 " ideal model delta sinusoidal sigma weight residual 220.00 45.07 174.93 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 99 " pdb=" C3' DT I 99 " pdb=" O3' DT I 99 " pdb=" P DA I 100 " ideal model delta sinusoidal sigma weight residual 220.00 64.06 155.94 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1879 0.035 - 0.069: 512 0.069 - 0.104: 103 0.104 - 0.138: 32 0.138 - 0.173: 7 Chirality restraints: 2533 Sorted by residual: chirality pdb=" C2' SAM K 402 " pdb=" C1' SAM K 402 " pdb=" C3' SAM K 402 " pdb=" O2' SAM K 402 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA ASP D 48 " pdb=" N ASP D 48 " pdb=" C ASP D 48 " pdb=" CB ASP D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 2530 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 231 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ILE K 231 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE K 231 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA K 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 264 " 0.013 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP K 264 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP K 264 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 264 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP K 264 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 264 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 264 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO F 32 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 426 2.67 - 3.23: 12770 3.23 - 3.78: 25319 3.78 - 4.34: 31896 4.34 - 4.90: 46915 Nonbonded interactions: 117326 Sorted by model distance: nonbonded pdb=" O THR K 284 " pdb=" OG1 THR K 288 " model vdw 2.111 2.440 nonbonded pdb=" O MET K 188 " pdb=" OG SER K 193 " model vdw 2.169 2.440 nonbonded pdb=" O2 DT I 157 " pdb=" N6 DA J 11 " model vdw 2.210 2.520 nonbonded pdb=" OG1 THR K 97 " pdb=" OD1 ASN K 208 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR K 97 " pdb=" O ASN K 208 " model vdw 2.231 2.440 ... (remaining 117321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 134) selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = (chain 'C' and resid 16 through 124) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 122)) 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 group one per residue 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 3.020 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 50.280 Find NCS groups from input model: 0.610 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: 0.010 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: 58.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.004 0.058 15620 Z= 0.226 Angle : 0.613 11.372 22444 Z= 0.357 Chirality : 0.035 0.173 2533 Planarity : 0.004 0.045 1733 Dihedral : 27.225 179.840 6653 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % 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 (0.27), residues: 1007 helix: 1.90 (0.22), residues: 598 sheet: -0.18 (0.84), residues: 22 loop : -2.15 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP K 264 HIS 0.004 0.001 HIS K 98 PHE 0.010 0.001 PHE K 281 TYR 0.025 0.001 TYR F 88 ARG 0.008 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.187 Fit side-chains REVERT: K 100 MET cc_start: 0.7208 (pmm) cc_final: 0.6878 (pmm) REVERT: E 76 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 95 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6652 (mm-30) REVERT: G 115 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7519 (tptp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.3137 time to fit residues: 69.8037 Evaluate side-chains 134 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.0010 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 181 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15620 Z= 0.195 Angle : 0.555 7.791 22444 Z= 0.327 Chirality : 0.034 0.146 2533 Planarity : 0.003 0.038 1733 Dihedral : 29.992 178.460 4658 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.41 % Allowed : 9.84 % Favored : 88.76 % 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: 0.93 (0.27), residues: 1007 helix: 2.15 (0.22), residues: 606 sheet: 0.56 (0.97), residues: 22 loop : -2.09 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 62 TYR 0.016 0.001 TYR F 88 ARG 0.004 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.187 Fit side-chains REVERT: K 100 MET cc_start: 0.7187 (pmm) cc_final: 0.6797 (pmm) REVERT: E 76 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8287 (tm-30) outliers start: 12 outliers final: 7 residues processed: 147 average time/residue: 0.2960 time to fit residues: 61.3691 Evaluate side-chains 136 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15620 Z= 0.320 Angle : 0.617 7.339 22444 Z= 0.361 Chirality : 0.037 0.151 2533 Planarity : 0.004 0.036 1733 Dihedral : 30.161 179.174 4658 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.11 % Allowed : 14.17 % Favored : 83.72 % 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: 0.63 (0.27), residues: 1007 helix: 1.91 (0.22), residues: 600 sheet: 0.62 (0.86), residues: 24 loop : -2.19 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 264 HIS 0.007 0.001 HIS F 75 PHE 0.011 0.001 PHE H 62 TYR 0.033 0.002 TYR H 80 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.094 Fit side-chains REVERT: K 100 MET cc_start: 0.7452 (pmm) cc_final: 0.6928 (pmm) REVERT: K 220 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.5172 (mmp-170) REVERT: E 76 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8173 (tm-30) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.3052 time to fit residues: 60.8770 Evaluate side-chains 138 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 220 ARG Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15620 Z= 0.282 Angle : 0.587 7.279 22444 Z= 0.345 Chirality : 0.036 0.148 2533 Planarity : 0.004 0.046 1733 Dihedral : 30.119 179.339 4658 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 2.22 % Allowed : 16.86 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1007 helix: 2.03 (0.22), residues: 599 sheet: 0.36 (0.75), residues: 24 loop : -2.20 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.004 0.001 HIS A 113 PHE 0.009 0.001 PHE H 62 TYR 0.021 0.001 TYR H 80 ARG 0.004 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.222 Fit side-chains REVERT: K 100 MET cc_start: 0.7351 (pmm) cc_final: 0.6883 (pmm) REVERT: E 76 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 0.3033 time to fit residues: 62.8117 Evaluate side-chains 145 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 107 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 0.0870 chunk 112 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15620 Z= 0.157 Angle : 0.514 5.960 22444 Z= 0.307 Chirality : 0.032 0.151 2533 Planarity : 0.003 0.040 1733 Dihedral : 29.989 178.544 4658 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 1.41 % Allowed : 17.92 % Favored : 80.68 % 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 (0.27), residues: 1007 helix: 2.41 (0.22), residues: 596 sheet: 0.91 (0.85), residues: 24 loop : -2.03 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.005 0.001 PHE B 61 TYR 0.011 0.001 TYR H 80 ARG 0.006 0.000 ARG K 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.125 Fit side-chains REVERT: K 100 MET cc_start: 0.7226 (pmm) cc_final: 0.6749 (pmm) REVERT: E 76 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8030 (tm-30) outliers start: 12 outliers final: 7 residues processed: 163 average time/residue: 0.2862 time to fit residues: 66.6947 Evaluate side-chains 148 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15620 Z= 0.201 Angle : 0.538 8.131 22444 Z= 0.318 Chirality : 0.033 0.150 2533 Planarity : 0.003 0.037 1733 Dihedral : 30.044 178.421 4658 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 1.87 % Allowed : 18.74 % Favored : 79.39 % 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: 1.07 (0.27), residues: 1007 helix: 2.34 (0.22), residues: 602 sheet: 0.62 (0.78), residues: 24 loop : -2.16 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 264 HIS 0.008 0.001 HIS G 112 PHE 0.022 0.001 PHE K 178 TYR 0.020 0.001 TYR H 80 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.225 Fit side-chains REVERT: K 100 MET cc_start: 0.7224 (pmm) cc_final: 0.6758 (pmm) REVERT: K 173 MET cc_start: 0.6173 (ppp) cc_final: 0.5378 (pmm) REVERT: E 76 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8013 (tm-30) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.2791 time to fit residues: 60.6280 Evaluate side-chains 146 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 0.1980 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15620 Z= 0.244 Angle : 0.559 6.956 22444 Z= 0.329 Chirality : 0.034 0.153 2533 Planarity : 0.004 0.036 1733 Dihedral : 30.069 178.289 4658 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 2.34 % Allowed : 18.85 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1007 helix: 2.23 (0.22), residues: 602 sheet: 0.32 (0.75), residues: 22 loop : -2.27 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 264 HIS 0.004 0.001 HIS K 98 PHE 0.015 0.001 PHE K 178 TYR 0.021 0.001 TYR H 80 ARG 0.004 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.192 Fit side-chains REVERT: K 100 MET cc_start: 0.7218 (pmm) cc_final: 0.6766 (pmm) REVERT: E 76 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7966 (tm-30) outliers start: 20 outliers final: 18 residues processed: 150 average time/residue: 0.2881 time to fit residues: 61.8334 Evaluate side-chains 150 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15620 Z= 0.245 Angle : 0.565 9.321 22444 Z= 0.331 Chirality : 0.034 0.146 2533 Planarity : 0.004 0.034 1733 Dihedral : 30.080 178.169 4658 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 3.04 % Allowed : 18.74 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 1007 helix: 2.25 (0.22), residues: 590 sheet: 0.66 (0.73), residues: 22 loop : -2.23 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 264 HIS 0.004 0.001 HIS A 113 PHE 0.031 0.001 PHE K 178 TYR 0.017 0.001 TYR H 80 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.148 Fit side-chains REVERT: K 100 MET cc_start: 0.7225 (pmm) cc_final: 0.6760 (pmm) REVERT: E 76 GLN cc_start: 0.8628 (tm-30) cc_final: 0.7962 (tm-30) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.2879 time to fit residues: 61.8010 Evaluate side-chains 150 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15620 Z= 0.252 Angle : 0.577 12.519 22444 Z= 0.335 Chirality : 0.035 0.154 2533 Planarity : 0.004 0.034 1733 Dihedral : 30.097 178.162 4658 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 2.58 % Allowed : 18.74 % Favored : 78.69 % 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: 0.80 (0.27), residues: 1007 helix: 2.18 (0.22), residues: 595 sheet: 0.67 (0.73), residues: 22 loop : -2.29 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.004 0.001 HIS A 113 PHE 0.033 0.001 PHE K 178 TYR 0.017 0.001 TYR H 80 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.250 Fit side-chains REVERT: K 100 MET cc_start: 0.7310 (pmm) cc_final: 0.6821 (pmm) REVERT: E 76 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7938 (tm-30) outliers start: 22 outliers final: 21 residues processed: 146 average time/residue: 0.2983 time to fit residues: 62.3822 Evaluate side-chains 153 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15620 Z= 0.295 Angle : 0.611 12.003 22444 Z= 0.352 Chirality : 0.036 0.152 2533 Planarity : 0.004 0.034 1733 Dihedral : 30.200 178.592 4658 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 2.81 % Allowed : 18.74 % Favored : 78.45 % 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: 0.66 (0.27), residues: 1007 helix: 2.07 (0.22), residues: 594 sheet: 0.65 (0.77), residues: 22 loop : -2.34 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.005 0.001 HIS A 113 PHE 0.009 0.001 PHE D 62 TYR 0.021 0.001 TYR H 80 ARG 0.005 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.179 Fit side-chains REVERT: K 100 MET cc_start: 0.7354 (pmm) cc_final: 0.6852 (pmm) REVERT: E 76 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8013 (tm-30) outliers start: 24 outliers final: 21 residues processed: 149 average time/residue: 0.2859 time to fit residues: 60.7625 Evaluate side-chains 151 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.0060 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092221 restraints weight = 33914.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092720 restraints weight = 25118.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092887 restraints weight = 16959.046| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15620 Z= 0.164 Angle : 0.544 11.683 22444 Z= 0.317 Chirality : 0.033 0.158 2533 Planarity : 0.003 0.052 1733 Dihedral : 30.094 177.350 4658 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 2.34 % Allowed : 19.20 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1007 helix: 2.36 (0.22), residues: 588 sheet: 0.48 (0.83), residues: 24 loop : -2.21 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.003 0.001 HIS K 98 PHE 0.005 0.001 PHE H 62 TYR 0.018 0.001 TYR H 80 ARG 0.006 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.27 seconds wall clock time: 40 minutes 4.73 seconds (2404.73 seconds total)