Starting phenix.real_space_refine on Mon Mar 11 11:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/03_2024/6pzi_20535_neut_updated.pdb" } resolution = 4.5 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 3 5.49 5 S 3 5.16 5 C 4968 2.51 5 N 1514 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 16": "NH1" <-> "NH2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 306": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7985 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1413, 7985 Unusual residues: {'ATP': 1} Classifications: {'peptide': 1412, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 991} Link IDs: {'PTRANS': 48, 'TRANS': 1363, None: 1} Not linked: pdbres="VAL G1578 " pdbres="ATP G1601 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3286 Unresolved non-hydrogen angles: 4184 Unresolved non-hydrogen dihedrals: 2582 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLN:plan1': 57, 'ARG:plan': 63, 'TYR:plan': 8, 'ASN:plan1': 37, 'TRP:plan': 6, 'HIS:plan': 13, 'PHE:plan': 51, 'GLU:plan': 56, 'ASP:plan': 51} Unresolved non-hydrogen planarities: 1512 Time building chain proxies: 5.68, per 1000 atoms: 0.71 Number of scatterers: 7985 At special positions: 0 Unit cell: (97.47, 112.86, 141.93, 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 3 16.00 P 3 15.00 O 1497 8.00 N 1514 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.03 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: 3.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 5 sheets defined 62.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'G' and resid 27 through 51 Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 72 through 98 Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 137 through 160 removed outlier: 3.584A pdb=" N LEU G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 193 Processing helix chain 'G' and resid 208 through 211 No H-bonds generated for 'chain 'G' and resid 208 through 211' Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 232 through 239 removed outlier: 3.676A pdb=" N PHE G 236 " --> pdb=" O TRP G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 257 No H-bonds generated for 'chain 'G' and resid 255 through 257' Processing helix chain 'G' and resid 259 through 276 Processing helix chain 'G' and resid 284 through 314 removed outlier: 5.451A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 348 through 351 No H-bonds generated for 'chain 'G' and resid 348 through 351' Processing helix chain 'G' and resid 356 through 399 removed outlier: 4.435A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 433 Processing helix chain 'G' and resid 437 through 455 Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 458 through 469 Processing helix chain 'G' and resid 471 through 504 removed outlier: 4.235A pdb=" N GLU G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 511 Processing helix chain 'G' and resid 516 through 547 removed outlier: 4.079A pdb=" N THR G 525 " --> pdb=" O ARG G 521 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER G 543 " --> pdb=" O TYR G 539 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 563 Processing helix chain 'G' and resid 573 through 614 Proline residue: G 589 - end of helix removed outlier: 4.223A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 719 through 726 Processing helix chain 'G' and resid 786 through 789 No H-bonds generated for 'chain 'G' and resid 786 through 789' Processing helix chain 'G' and resid 796 through 805 Processing helix chain 'G' and resid 809 through 814 Processing helix chain 'G' and resid 832 through 845 Processing helix chain 'G' and resid 863 through 880 Processing helix chain 'G' and resid 914 through 917 No H-bonds generated for 'chain 'G' and resid 914 through 917' Processing helix chain 'G' and resid 923 through 926 No H-bonds generated for 'chain 'G' and resid 923 through 926' Processing helix chain 'G' and resid 997 through 1008 Processing helix chain 'G' and resid 1010 through 1042 removed outlier: 4.262A pdb=" N LEU G1015 " --> pdb=" O LEU G1011 " (cutoff:3.500A) Processing helix chain 'G' and resid 1061 through 1106 removed outlier: 3.699A pdb=" N LEU G1074 " --> pdb=" O LEU G1070 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU G1087 " --> pdb=" O SER G1083 " (cutoff:3.500A) Processing helix chain 'G' and resid 1110 through 1115 Processing helix chain 'G' and resid 1118 through 1134 removed outlier: 4.387A pdb=" N ASP G1128 " --> pdb=" O ARG G1124 " (cutoff:3.500A) Processing helix chain 'G' and resid 1136 through 1160 removed outlier: 4.053A pdb=" N LEU G1148 " --> pdb=" O SER G1144 " (cutoff:3.500A) Processing helix chain 'G' and resid 1164 through 1209 Proline residue: G1170 - end of helix removed outlier: 4.008A pdb=" N ASP G1188 " --> pdb=" O VAL G1184 " (cutoff:3.500A) Proline residue: G1199 - end of helix Processing helix chain 'G' and resid 1211 through 1216 Processing helix chain 'G' and resid 1220 through 1272 removed outlier: 3.788A pdb=" N ALA G1237 " --> pdb=" O SER G1233 " (cutoff:3.500A) Processing helix chain 'G' and resid 1279 through 1319 removed outlier: 4.501A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G1314 " --> pdb=" O GLY G1310 " (cutoff:3.500A) Processing helix chain 'G' and resid 1332 through 1338 Proline residue: G1336 - end of helix No H-bonds generated for 'chain 'G' and resid 1332 through 1338' Processing helix chain 'G' and resid 1386 through 1393 removed outlier: 4.284A pdb=" N PHE G1393 " --> pdb=" O SER G1389 " (cutoff:3.500A) Processing helix chain 'G' and resid 1415 through 1418 No H-bonds generated for 'chain 'G' and resid 1415 through 1418' Processing helix chain 'G' and resid 1436 through 1441 Processing helix chain 'G' and resid 1448 through 1457 Processing helix chain 'G' and resid 1461 through 1464 No H-bonds generated for 'chain 'G' and resid 1461 through 1464' Processing helix chain 'G' and resid 1485 through 1497 Processing helix chain 'G' and resid 1513 through 1529 Processing helix chain 'G' and resid 1540 through 1542 No H-bonds generated for 'chain 'G' and resid 1540 through 1542' Processing helix chain 'G' and resid 1564 through 1569 Processing helix chain 'G' and resid 1571 through 1575 Processing sheet with id= A, first strand: chain 'G' and resid 338 through 340 removed outlier: 3.928A pdb=" N THR G 338 " --> pdb=" O PHE G 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 679 through 681 Processing sheet with id= C, first strand: chain 'G' and resid 907 through 910 removed outlier: 6.910A pdb=" N ALA G 902 " --> pdb=" O GLN G 909 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 884 " --> pdb=" O THR G 709 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE G 711 " --> pdb=" O VAL G 884 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU G 886 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY G 713 " --> pdb=" O LEU G 886 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 1346 through 1348 Processing sheet with id= E, first strand: chain 'G' and resid 1549 through 1551 647 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2848 1.34 - 1.46: 1845 1.46 - 1.58: 3440 1.58 - 1.70: 5 1.70 - 1.82: 3 Bond restraints: 8141 Sorted by residual: bond pdb=" C4 ATP G1601 " pdb=" C5 ATP G1601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.80e+01 bond pdb=" C5 ATP G1601 " pdb=" C6 ATP G1601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP G1601 " pdb=" N7 ATP G1601 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.91e+01 bond pdb=" C4 ATP G1601 " pdb=" N9 ATP G1601 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.81e+01 bond pdb=" C8 ATP G1601 " pdb=" N7 ATP G1601 " ideal model delta sigma weight residual 1.310 1.348 -0.038 1.00e-02 1.00e+04 1.47e+01 ... (remaining 8136 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.67: 267 106.67 - 114.01: 4420 114.01 - 121.34: 4410 121.34 - 128.68: 2155 128.68 - 136.01: 81 Bond angle restraints: 11333 Sorted by residual: angle pdb=" PA ATP G1601 " pdb=" O3A ATP G1601 " pdb=" PB ATP G1601 " ideal model delta sigma weight residual 136.83 115.25 21.58 1.00e+00 1.00e+00 4.66e+02 angle pdb=" PB ATP G1601 " pdb=" O3B ATP G1601 " pdb=" PG ATP G1601 " ideal model delta sigma weight residual 139.87 121.63 18.24 1.00e+00 1.00e+00 3.33e+02 angle pdb=" C5' ATP G1601 " pdb=" O5' ATP G1601 " pdb=" PA ATP G1601 " ideal model delta sigma weight residual 121.27 109.37 11.90 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C5 ATP G1601 " pdb=" C4 ATP G1601 " pdb=" N3 ATP G1601 " ideal model delta sigma weight residual 126.80 118.39 8.41 1.00e+00 1.00e+00 7.07e+01 angle pdb=" O3A ATP G1601 " pdb=" PA ATP G1601 " pdb=" O5' ATP G1601 " ideal model delta sigma weight residual 102.67 120.99 -18.32 2.38e+00 1.77e-01 5.92e+01 ... (remaining 11328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4554 17.76 - 35.51: 78 35.51 - 53.27: 17 53.27 - 71.02: 2 71.02 - 88.78: 1 Dihedral angle restraints: 4652 sinusoidal: 543 harmonic: 4109 Sorted by residual: dihedral pdb=" CA ILE G 996 " pdb=" C ILE G 996 " pdb=" N PRO G 997 " pdb=" CA PRO G 997 " ideal model delta harmonic sigma weight residual -180.00 -142.55 -37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 26 " pdb=" CB CYS G 26 " ideal model delta sinusoidal sigma weight residual 93.00 143.69 -50.69 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA LYS G1562 " pdb=" C LYS G1562 " pdb=" N PRO G1563 " pdb=" CA PRO G1563 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 926 0.046 - 0.092: 356 0.092 - 0.138: 86 0.138 - 0.184: 13 0.184 - 0.231: 7 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB VAL G1352 " pdb=" CA VAL G1352 " pdb=" CG1 VAL G1352 " pdb=" CG2 VAL G1352 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TRP G1297 " pdb=" N TRP G1297 " pdb=" C TRP G1297 " pdb=" CB TRP G1297 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TRP G1339 " pdb=" N TRP G1339 " pdb=" C TRP G1339 " pdb=" CB TRP G1339 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1385 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G1311 " 0.035 2.00e-02 2.50e+03 6.95e-02 4.84e+01 pdb=" C ALA G1311 " -0.120 2.00e-02 2.50e+03 pdb=" O ALA G1311 " 0.045 2.00e-02 2.50e+03 pdb=" N VAL G1312 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G1286 " -0.030 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C THR G1286 " 0.102 2.00e-02 2.50e+03 pdb=" O THR G1286 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR G1287 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 94 " 0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LEU G 94 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU G 94 " 0.030 2.00e-02 2.50e+03 pdb=" N SER G 95 " 0.028 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2123 2.78 - 3.31: 7766 3.31 - 3.84: 13150 3.84 - 4.37: 12770 4.37 - 4.90: 22252 Nonbonded interactions: 58061 Sorted by model distance: nonbonded pdb=" O ALA G1288 " pdb=" OG SER G1292 " model vdw 2.253 2.440 nonbonded pdb=" O THR G 789 " pdb=" OG SER G 792 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR G 123 " pdb=" O LEU G 135 " model vdw 2.279 2.440 nonbonded pdb=" O LEU G 39 " pdb=" OG1 THR G 43 " model vdw 2.293 2.440 nonbonded pdb=" O ALA G 235 " pdb=" OG1 THR G 239 " model vdw 2.303 2.440 ... (remaining 58056 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: 0.450 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: 1.630 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.082 8141 Z= 0.370 Angle : 1.133 21.583 11333 Z= 0.721 Chirality : 0.052 0.231 1388 Planarity : 0.010 0.070 1573 Dihedral : 9.013 88.779 1975 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.18), residues: 1400 helix: -1.92 (0.13), residues: 907 sheet: -3.79 (0.50), residues: 61 loop : -3.40 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP G1297 HIS 0.022 0.004 HIS G1098 PHE 0.038 0.002 PHE G 433 TYR 0.042 0.003 TYR G1294 ARG 0.019 0.002 ARG G 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8910 (tpt-90) cc_final: 0.8609 (tpt-90) REVERT: G 363 PHE cc_start: 0.8968 (t80) cc_final: 0.8725 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1769 time to fit residues: 15.7235 Evaluate side-chains 52 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.0870 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.0050 chunk 82 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 overall best weight: 2.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 HIS ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8141 Z= 0.156 Angle : 0.529 8.255 11333 Z= 0.290 Chirality : 0.040 0.135 1388 Planarity : 0.005 0.056 1573 Dihedral : 5.626 67.580 1478 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1400 helix: 0.65 (0.16), residues: 918 sheet: -3.11 (0.58), residues: 60 loop : -2.93 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G1297 HIS 0.010 0.001 HIS G1098 PHE 0.016 0.001 PHE G 433 TYR 0.014 0.001 TYR G 378 ARG 0.002 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8905 (tpt-90) cc_final: 0.8546 (mmm160) REVERT: G 363 PHE cc_start: 0.9017 (t80) cc_final: 0.8795 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1190 time to fit residues: 11.4889 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN G 817 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8141 Z= 0.317 Angle : 0.627 7.520 11333 Z= 0.366 Chirality : 0.042 0.155 1388 Planarity : 0.005 0.052 1573 Dihedral : 5.803 70.017 1478 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.42 % Allowed : 3.39 % Favored : 96.19 % 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: 0.31 (0.23), residues: 1400 helix: 1.65 (0.17), residues: 917 sheet: -2.37 (0.75), residues: 51 loop : -2.80 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 288 HIS 0.010 0.002 HIS G1098 PHE 0.016 0.002 PHE G 613 TYR 0.022 0.002 TYR G 124 ARG 0.008 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9069 (tpt-90) cc_final: 0.8621 (mmm160) REVERT: G 394 LYS cc_start: 0.9775 (tptm) cc_final: 0.9468 (tppt) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1215 time to fit residues: 11.0412 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0070 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 136 optimal weight: 40.0000 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8141 Z= 0.225 Angle : 0.534 6.687 11333 Z= 0.301 Chirality : 0.041 0.146 1388 Planarity : 0.004 0.046 1573 Dihedral : 5.326 84.743 1478 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1400 helix: 2.33 (0.17), residues: 922 sheet: -2.39 (0.68), residues: 58 loop : -2.45 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.027 0.002 PHE G1240 TYR 0.013 0.001 TYR G 378 ARG 0.005 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1387 time to fit residues: 11.6038 Evaluate side-chains 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 116 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8141 Z= 0.255 Angle : 0.554 6.531 11333 Z= 0.316 Chirality : 0.041 0.145 1388 Planarity : 0.004 0.049 1573 Dihedral : 5.353 86.703 1478 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 1.34 (0.24), residues: 1400 helix: 2.46 (0.17), residues: 914 sheet: -2.38 (0.70), residues: 57 loop : -2.31 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.026 0.002 PHE G 518 TYR 0.013 0.002 TYR G 475 ARG 0.006 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9060 (tpt-90) cc_final: 0.8652 (mmm160) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1140 time to fit residues: 9.6952 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 491 HIS G 584 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8141 Z= 0.338 Angle : 0.618 7.204 11333 Z= 0.363 Chirality : 0.042 0.139 1388 Planarity : 0.005 0.054 1573 Dihedral : 5.793 84.310 1478 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 0.77 (0.23), residues: 1400 helix: 1.96 (0.17), residues: 919 sheet: -2.24 (0.79), residues: 45 loop : -2.51 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 288 HIS 0.009 0.002 HIS G1098 PHE 0.023 0.002 PHE G 518 TYR 0.018 0.002 TYR G 475 ARG 0.007 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1164 time to fit residues: 10.1878 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 0.0020 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8141 Z= 0.262 Angle : 0.561 6.472 11333 Z= 0.319 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.050 1573 Dihedral : 5.520 84.708 1478 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 1.12 (0.23), residues: 1400 helix: 2.22 (0.17), residues: 919 sheet: -2.08 (0.81), residues: 45 loop : -2.35 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.018 0.001 PHE G 518 TYR 0.015 0.002 TYR G 475 ARG 0.007 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9055 (tpt-90) cc_final: 0.8632 (mmm160) REVERT: G 394 LYS cc_start: 0.9822 (tptm) cc_final: 0.9508 (tppt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1165 time to fit residues: 10.1509 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 123 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8141 Z= 0.327 Angle : 0.616 7.189 11333 Z= 0.360 Chirality : 0.042 0.158 1388 Planarity : 0.004 0.064 1573 Dihedral : 5.730 83.995 1478 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 0.69 (0.23), residues: 1400 helix: 1.91 (0.17), residues: 913 sheet: -1.53 (0.92), residues: 40 loop : -2.59 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP G1297 HIS 0.008 0.002 HIS G 71 PHE 0.024 0.002 PHE G 518 TYR 0.019 0.002 TYR G 475 ARG 0.007 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8949 (tpt-90) cc_final: 0.8514 (mmm160) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1154 time to fit residues: 10.0471 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0170 chunk 130 optimal weight: 8.9990 chunk 76 optimal weight: 0.0670 chunk 55 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 81 optimal weight: 30.0000 overall best weight: 3.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8141 Z= 0.204 Angle : 0.531 8.088 11333 Z= 0.294 Chirality : 0.041 0.150 1388 Planarity : 0.004 0.048 1573 Dihedral : 5.265 82.122 1478 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.41 (0.23), residues: 1400 helix: 2.49 (0.17), residues: 913 sheet: -1.72 (0.84), residues: 45 loop : -2.32 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.015 0.001 PHE G 518 TYR 0.013 0.001 TYR G 475 ARG 0.007 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8983 (tpt-90) cc_final: 0.8578 (mmm160) REVERT: G 394 LYS cc_start: 0.9801 (tptm) cc_final: 0.9477 (tppt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1452 time to fit residues: 12.0233 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0060 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8141 Z= 0.223 Angle : 0.537 6.842 11333 Z= 0.301 Chirality : 0.041 0.149 1388 Planarity : 0.004 0.047 1573 Dihedral : 5.180 80.761 1478 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.50 (0.23), residues: 1400 helix: 2.61 (0.17), residues: 906 sheet: -1.41 (0.93), residues: 41 loop : -2.35 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G1297 HIS 0.006 0.001 HIS G1098 PHE 0.028 0.001 PHE G1240 TYR 0.013 0.001 TYR G 475 ARG 0.005 0.001 ARG G 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8973 (tpt-90) cc_final: 0.8578 (mmm160) REVERT: G 394 LYS cc_start: 0.9808 (tptm) cc_final: 0.9474 (tppt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1147 time to fit residues: 10.1070 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 80 optimal weight: 9.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** 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 = 0.2833 r_free = 0.2833 target = 0.038306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032574 restraints weight = 98550.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033151 restraints weight = 68688.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033590 restraints weight = 51270.855| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8141 Z= 0.134 Angle : 0.489 10.400 11333 Z= 0.259 Chirality : 0.040 0.155 1388 Planarity : 0.003 0.046 1573 Dihedral : 4.757 78.494 1478 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.16 (0.24), residues: 1400 helix: 3.16 (0.17), residues: 911 sheet: -1.34 (0.93), residues: 41 loop : -2.24 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.016 0.001 PHE G1240 TYR 0.012 0.001 TYR G1219 ARG 0.003 0.001 ARG G 168 =============================================================================== Job complete usr+sys time: 1251.37 seconds wall clock time: 23 minutes 18.98 seconds (1398.98 seconds total)