Starting phenix.real_space_refine on Thu Feb 15 05:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atw_15665/02_2024/8atw_15665_updated.pdb" } resolution = 3.62 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= 0.013 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 36 5.16 5 C 7024 2.51 5 N 1957 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 1131": "OE1" <-> "OE2" Residue "A GLU 1223": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7235 Classifications: {'peptide': 922} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 582 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 567 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.59 Number of scatterers: 11283 At special positions: 0 Unit cell: (106.7, 114.46, 118.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 64 15.00 O 2202 8.00 N 1957 7.00 C 7024 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 9 sheets defined 51.9% alpha, 7.9% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 removed outlier: 4.100A pdb=" N LYS B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.722A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 4.152A pdb=" N GLU B 144 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY B 145 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 274 through 280 removed outlier: 4.262A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 280' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 398 through 420 removed outlier: 3.747A pdb=" N GLN A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 447 through 477 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.062A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 505 through 518 Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.646A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 Processing helix chain 'A' and resid 653 through 662 removed outlier: 4.427A pdb=" N GLY A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 776 through 812 Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 914 through 929 Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 978 through 993 Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.285A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1048 through 1065 Processing helix chain 'A' and resid 1069 through 1084 Processing helix chain 'A' and resid 1091 through 1093 No H-bonds generated for 'chain 'A' and resid 1091 through 1093' Processing helix chain 'A' and resid 1150 through 1180 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1217 through 1228 Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.869A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1279 Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1296 through 1302 removed outlier: 3.984A pdb=" N ASP A1302 " --> pdb=" O SER A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1309 No H-bonds generated for 'chain 'A' and resid 1306 through 1309' Processing helix chain 'A' and resid 1341 through 1345 removed outlier: 4.003A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 200 through 204 removed outlier: 3.572A pdb=" N ASP B 248 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS B 49 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N VAL B 135 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 51 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASN B 137 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 53 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 72 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP B 52 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER B 74 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLN B 96 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 530 Processing sheet with id= C, first strand: chain 'A' and resid 613 through 620 removed outlier: 3.641A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 620 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 625 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= E, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= F, first strand: chain 'A' and resid 942 through 944 Processing sheet with id= G, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= H, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.517A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1233 through 1238 removed outlier: 3.530A pdb=" N VAL A1323 " --> pdb=" O GLY A1236 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 5.53 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: 2617 1.33 - 1.45: 2671 1.45 - 1.57: 6212 1.57 - 1.69: 116 1.69 - 1.81: 61 Bond restraints: 11677 Sorted by residual: bond pdb=" O3' DT N 109 " pdb=" P DA N 110 " ideal model delta sigma weight residual 1.607 1.436 0.171 1.50e-02 4.44e+03 1.30e+02 bond pdb=" C4' DT T 20 " pdb=" O4' DT T 20 " ideal model delta sigma weight residual 1.450 1.621 -0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C4' DT T 21 " pdb=" O4' DT T 21 " ideal model delta sigma weight residual 1.450 1.568 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sigma weight residual 1.607 1.690 -0.083 1.50e-02 4.44e+03 3.03e+01 bond pdb=" O3' DA T 27 " pdb=" P DA T 28 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.03e+01 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.41: 238 103.41 - 111.09: 4807 111.09 - 118.78: 4767 118.78 - 126.46: 5883 126.46 - 134.15: 399 Bond angle restraints: 16094 Sorted by residual: angle pdb=" C5' DA T 34 " pdb=" C4' DA T 34 " pdb=" O4' DA T 34 " ideal model delta sigma weight residual 109.40 123.30 -13.90 1.50e+00 4.44e-01 8.59e+01 angle pdb=" O3' DA T 28 " pdb=" C3' DA T 28 " pdb=" C2' DA T 28 " ideal model delta sigma weight residual 111.50 98.72 12.78 1.50e+00 4.44e-01 7.25e+01 angle pdb=" C5' DT N 112 " pdb=" C4' DT N 112 " pdb=" O4' DT N 112 " ideal model delta sigma weight residual 109.40 121.24 -11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" C5' DT T 29 " pdb=" C4' DT T 29 " pdb=" O4' DT T 29 " ideal model delta sigma weight residual 109.40 119.88 -10.48 1.50e+00 4.44e-01 4.88e+01 angle pdb=" O4' DT T 20 " pdb=" C4' DT T 20 " pdb=" C3' DT T 20 " ideal model delta sigma weight residual 105.40 95.72 9.68 1.50e+00 4.44e-01 4.16e+01 ... (remaining 16089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 6053 21.65 - 43.30: 641 43.30 - 64.95: 169 64.95 - 86.60: 20 86.60 - 108.26: 5 Dihedral angle restraints: 6888 sinusoidal: 3214 harmonic: 3674 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual 274.12 165.87 108.26 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 2.87 101.72 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" CA MET B 267 " pdb=" C MET B 267 " pdb=" N ILE B 268 " pdb=" CA ILE B 268 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1756 0.131 - 0.262: 16 0.262 - 0.393: 6 0.393 - 0.524: 2 0.524 - 0.655: 2 Chirality restraints: 1782 Sorted by residual: chirality pdb=" C4' DT T 20 " pdb=" C5' DT T 20 " pdb=" O4' DT T 20 " pdb=" C3' DT T 20 " both_signs ideal model delta sigma weight residual False -2.53 -3.18 0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DG N 108 " pdb=" OP1 DG N 108 " pdb=" OP2 DG N 108 " pdb=" O5' DG N 108 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4' DT T 29 " pdb=" C5' DT T 29 " pdb=" O4' DT T 29 " pdb=" C3' DT T 29 " both_signs ideal model delta sigma weight residual False -2.53 -2.02 -0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 1779 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 28 " -0.022 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA T 28 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA T 28 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 28 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA T 28 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA T 28 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 272 " -0.033 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 273 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 120 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.020 5.00e-02 4.00e+02 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 832 2.74 - 3.28: 11236 3.28 - 3.82: 19584 3.82 - 4.36: 22401 4.36 - 4.90: 37663 Nonbonded interactions: 91716 Sorted by model distance: nonbonded pdb=" O LEU B 23 " pdb=" OH TYR B 29 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.210 2.440 nonbonded pdb=" NH2 ARG A1206 " pdb=" O SER A1346 " model vdw 2.260 2.520 nonbonded pdb=" OD2 ASP A 775 " pdb=" OG SER A 777 " model vdw 2.276 2.440 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.283 2.440 ... (remaining 91711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.080 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: 1.160 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 37.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 11677 Z= 0.265 Angle : 0.737 13.899 16094 Z= 0.407 Chirality : 0.054 0.655 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.135 108.255 4508 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 1.06 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 708 sheet: 0.27 (0.56), residues: 85 loop : -0.58 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 159 HIS 0.004 0.001 HIS A1169 PHE 0.020 0.001 PHE A1300 TYR 0.021 0.002 TYR A 979 ARG 0.007 0.000 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.284 Fit side-chains REVERT: B 52 ASP cc_start: 0.6643 (t70) cc_final: 0.6442 (t70) REVERT: B 71 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7430 (ptt180) REVERT: B 247 MET cc_start: 0.8059 (mmt) cc_final: 0.7852 (mmp) REVERT: A 398 LEU cc_start: 0.8355 (mt) cc_final: 0.8045 (mt) REVERT: A 402 LYS cc_start: 0.8556 (mptt) cc_final: 0.8352 (mptt) REVERT: A 514 LEU cc_start: 0.8787 (mt) cc_final: 0.7974 (tp) REVERT: A 1057 HIS cc_start: 0.6975 (m90) cc_final: 0.6355 (m90) REVERT: A 1325 LEU cc_start: 0.8353 (mm) cc_final: 0.8106 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2256 time to fit residues: 67.2698 Evaluate side-chains 153 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11677 Z= 0.220 Angle : 0.554 8.797 16094 Z= 0.291 Chirality : 0.039 0.173 1782 Planarity : 0.004 0.040 1838 Dihedral : 18.381 98.687 2081 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 9.32 % Favored : 89.19 % 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: 1.08 (0.24), residues: 1250 helix: 1.66 (0.20), residues: 705 sheet: 0.39 (0.44), residues: 122 loop : -0.77 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1110 HIS 0.005 0.001 HIS B 265 PHE 0.015 0.001 PHE A 886 TYR 0.017 0.001 TYR A1229 ARG 0.007 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.276 Fit side-chains REVERT: B 71 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.7438 (ptt180) REVERT: A 514 LEU cc_start: 0.8832 (mt) cc_final: 0.8073 (tp) REVERT: A 873 PHE cc_start: 0.8759 (m-80) cc_final: 0.8485 (m-80) REVERT: A 998 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: A 1057 HIS cc_start: 0.7062 (m90) cc_final: 0.6465 (m90) REVERT: A 1096 PHE cc_start: 0.7669 (p90) cc_final: 0.7457 (p90) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 0.2057 time to fit residues: 53.6107 Evaluate side-chains 157 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 0.0970 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 4.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11677 Z= 0.250 Angle : 0.549 9.422 16094 Z= 0.288 Chirality : 0.039 0.170 1782 Planarity : 0.004 0.042 1838 Dihedral : 18.453 101.822 2081 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.33 % Allowed : 12.02 % Favored : 85.65 % 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: 1.01 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 697 sheet: 0.22 (0.44), residues: 127 loop : -0.79 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 24 HIS 0.007 0.001 HIS B 265 PHE 0.016 0.001 PHE A1138 TYR 0.013 0.001 TYR B 161 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: B 71 ARG cc_start: 0.7675 (ptp-110) cc_final: 0.7446 (ptt180) REVERT: B 319 MET cc_start: 0.8467 (mmp) cc_final: 0.8233 (mmp) REVERT: A 998 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: A 1057 HIS cc_start: 0.7127 (m90) cc_final: 0.6545 (m90) REVERT: A 1096 PHE cc_start: 0.7561 (p90) cc_final: 0.7346 (p90) outliers start: 25 outliers final: 22 residues processed: 173 average time/residue: 0.2166 time to fit residues: 55.5492 Evaluate side-chains 166 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 20.0000 chunk 88 optimal weight: 0.0270 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11677 Z= 0.205 Angle : 0.524 8.396 16094 Z= 0.274 Chirality : 0.038 0.170 1782 Planarity : 0.004 0.038 1838 Dihedral : 18.388 103.111 2081 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.61 % Allowed : 14.45 % Favored : 82.95 % 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: 1.02 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 695 sheet: 0.22 (0.44), residues: 127 loop : -0.75 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 PHE 0.014 0.001 PHE A1300 TYR 0.011 0.001 TYR B 161 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: B 319 MET cc_start: 0.8423 (mmp) cc_final: 0.8176 (mmp) REVERT: A 998 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: A 1057 HIS cc_start: 0.7061 (m90) cc_final: 0.6471 (m90) REVERT: A 1096 PHE cc_start: 0.7517 (p90) cc_final: 0.7269 (p90) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.2091 time to fit residues: 52.8122 Evaluate side-chains 166 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11677 Z= 0.252 Angle : 0.544 8.113 16094 Z= 0.285 Chirality : 0.039 0.156 1782 Planarity : 0.004 0.061 1838 Dihedral : 18.420 106.485 2081 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.54 % Allowed : 15.00 % Favored : 81.45 % 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: 0.90 (0.24), residues: 1250 helix: 1.57 (0.20), residues: 686 sheet: 0.20 (0.44), residues: 127 loop : -0.81 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 24 HIS 0.005 0.001 HIS B 265 PHE 0.014 0.001 PHE A1300 TYR 0.012 0.001 TYR B 161 ARG 0.003 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: B 130 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8260 (p0) REVERT: B 319 MET cc_start: 0.8422 (mmp) cc_final: 0.8187 (mmp) REVERT: A 529 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7924 (ppp) REVERT: A 998 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: A 1057 HIS cc_start: 0.7075 (m90) cc_final: 0.6478 (m90) REVERT: A 1096 PHE cc_start: 0.7475 (p90) cc_final: 0.7124 (p90) outliers start: 38 outliers final: 26 residues processed: 172 average time/residue: 0.2232 time to fit residues: 57.0174 Evaluate side-chains 168 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 0.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11677 Z= 0.179 Angle : 0.527 8.963 16094 Z= 0.273 Chirality : 0.038 0.160 1782 Planarity : 0.004 0.069 1838 Dihedral : 18.309 106.690 2081 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.26 % Allowed : 16.87 % Favored : 79.87 % 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: 1.02 (0.24), residues: 1250 helix: 1.66 (0.20), residues: 686 sheet: 0.23 (0.44), residues: 127 loop : -0.73 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 24 HIS 0.003 0.001 HIS B 265 PHE 0.012 0.001 PHE A1300 TYR 0.015 0.001 TYR A1229 ARG 0.004 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: B 255 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7519 (p0) REVERT: A 529 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7879 (ppp) REVERT: A 1057 HIS cc_start: 0.6991 (m90) cc_final: 0.6408 (m90) REVERT: A 1096 PHE cc_start: 0.7391 (p90) cc_final: 0.7012 (p90) REVERT: A 1300 PHE cc_start: 0.7200 (t80) cc_final: 0.6902 (t80) outliers start: 35 outliers final: 25 residues processed: 179 average time/residue: 0.2111 time to fit residues: 55.9699 Evaluate side-chains 168 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 40.0000 chunk 76 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11677 Z= 0.238 Angle : 0.553 8.319 16094 Z= 0.287 Chirality : 0.038 0.160 1782 Planarity : 0.004 0.048 1838 Dihedral : 18.389 107.810 2081 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.98 % Allowed : 17.80 % Favored : 79.22 % 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: 0.96 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 684 sheet: 0.24 (0.45), residues: 126 loop : -0.72 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 24 HIS 0.005 0.001 HIS B 265 PHE 0.018 0.001 PHE B 85 TYR 0.019 0.002 TYR B 73 ARG 0.002 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.199 Fit side-chains REVERT: B 320 GLU cc_start: 0.7787 (mp0) cc_final: 0.7509 (mp0) REVERT: A 529 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7894 (ppp) REVERT: A 952 GLN cc_start: 0.7978 (mt0) cc_final: 0.7746 (mt0) REVERT: A 1057 HIS cc_start: 0.7006 (m90) cc_final: 0.6399 (m90) REVERT: A 1096 PHE cc_start: 0.7393 (p90) cc_final: 0.7059 (p90) outliers start: 32 outliers final: 26 residues processed: 170 average time/residue: 0.2079 time to fit residues: 52.8543 Evaluate side-chains 168 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 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 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11677 Z= 0.249 Angle : 0.568 8.925 16094 Z= 0.293 Chirality : 0.039 0.148 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.419 109.904 2081 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.26 % Allowed : 18.36 % Favored : 78.38 % 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: 0.94 (0.24), residues: 1250 helix: 1.58 (0.20), residues: 682 sheet: 0.42 (0.45), residues: 120 loop : -0.78 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 24 HIS 0.005 0.001 HIS B 265 PHE 0.021 0.001 PHE B 85 TYR 0.018 0.002 TYR B 73 ARG 0.004 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.230 Fit side-chains REVERT: B 130 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8266 (p0) REVERT: B 329 MET cc_start: 0.6832 (mtm) cc_final: 0.6349 (mmm) REVERT: A 529 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7903 (ppp) REVERT: A 952 GLN cc_start: 0.7983 (mt0) cc_final: 0.7747 (mt0) REVERT: A 1057 HIS cc_start: 0.7031 (m90) cc_final: 0.6428 (m90) REVERT: A 1096 PHE cc_start: 0.7363 (p90) cc_final: 0.7004 (p90) outliers start: 35 outliers final: 29 residues processed: 174 average time/residue: 0.2191 time to fit residues: 56.3576 Evaluate side-chains 173 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11677 Z= 0.156 Angle : 0.535 9.449 16094 Z= 0.275 Chirality : 0.037 0.158 1782 Planarity : 0.004 0.050 1838 Dihedral : 18.185 108.236 2081 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 19.11 % Favored : 78.29 % 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 (0.24), residues: 1250 helix: 1.75 (0.20), residues: 682 sheet: 0.54 (0.46), residues: 120 loop : -0.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 24 HIS 0.002 0.001 HIS A1169 PHE 0.015 0.001 PHE B 85 TYR 0.018 0.001 TYR B 73 ARG 0.005 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.229 Fit side-chains REVERT: B 319 MET cc_start: 0.8286 (mmp) cc_final: 0.8041 (mmp) REVERT: B 320 GLU cc_start: 0.7792 (mp0) cc_final: 0.7380 (mp0) REVERT: B 329 MET cc_start: 0.6837 (mtm) cc_final: 0.6355 (mmm) REVERT: A 529 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7814 (ppp) REVERT: A 1057 HIS cc_start: 0.7014 (m90) cc_final: 0.6380 (m90) REVERT: A 1096 PHE cc_start: 0.7274 (p90) cc_final: 0.6978 (p90) REVERT: A 1300 PHE cc_start: 0.7269 (t80) cc_final: 0.6979 (t80) outliers start: 28 outliers final: 20 residues processed: 187 average time/residue: 0.2120 time to fit residues: 58.2833 Evaluate side-chains 171 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 85 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11677 Z= 0.179 Angle : 0.548 9.707 16094 Z= 0.283 Chirality : 0.037 0.143 1782 Planarity : 0.004 0.048 1838 Dihedral : 18.165 107.591 2081 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.96 % Allowed : 20.13 % Favored : 77.91 % 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: 1.18 (0.24), residues: 1250 helix: 1.74 (0.20), residues: 681 sheet: 0.57 (0.45), residues: 115 loop : -0.59 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 24 HIS 0.002 0.001 HIS A1169 PHE 0.014 0.001 PHE B 85 TYR 0.013 0.001 TYR B 73 ARG 0.002 0.000 ARG A1275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.307 Fit side-chains REVERT: B 329 MET cc_start: 0.6856 (mtm) cc_final: 0.6361 (mmm) REVERT: A 529 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7683 (ppp) REVERT: A 1057 HIS cc_start: 0.7046 (m90) cc_final: 0.6432 (m90) REVERT: A 1096 PHE cc_start: 0.7249 (p90) cc_final: 0.6948 (p90) REVERT: A 1300 PHE cc_start: 0.7255 (t80) cc_final: 0.6988 (t80) outliers start: 21 outliers final: 19 residues processed: 169 average time/residue: 0.2210 time to fit residues: 55.3300 Evaluate side-chains 168 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 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 = 0.3786 r_free = 0.3786 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113881 restraints weight = 17987.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117354 restraints weight = 10144.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119674 restraints weight = 7219.015| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11677 Z= 0.230 Angle : 0.569 9.802 16094 Z= 0.293 Chirality : 0.038 0.138 1782 Planarity : 0.004 0.048 1838 Dihedral : 18.260 108.287 2081 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.33 % Allowed : 19.85 % Favored : 77.82 % 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: 1.10 (0.24), residues: 1250 helix: 1.67 (0.20), residues: 682 sheet: 0.50 (0.45), residues: 120 loop : -0.64 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 24 HIS 0.004 0.001 HIS B 265 PHE 0.015 0.001 PHE B 85 TYR 0.015 0.001 TYR B 73 ARG 0.007 0.000 ARG A1275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.40 seconds wall clock time: 38 minutes 3.39 seconds (2283.39 seconds total)