Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 19:06:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzb_20533/10_2023/6pzb_20533_neut.pdb" } resolution = 4.55 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= 0.002 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 4834 2.51 5 N 1468 2.21 5 O 1440 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 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "G ARG 1104": "NH1" <-> "NH2" Residue "G ARG 1218": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 7747 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 7747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 7747 Classifications: {'peptide': 1357} Incomplete info: {'truncation_to_alanine': 915} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 1313} Chain breaks: 11 Unresolved non-hydrogen bonds: 3073 Unresolved non-hydrogen angles: 3921 Unresolved non-hydrogen dihedrals: 2428 Unresolved non-hydrogen chiralities: 416 Planarities with less than four sites: {'GLN:plan1': 52, 'ARG:plan': 58, 'TYR:plan': 12, 'ASN:plan1': 36, 'TRP:plan': 7, 'HIS:plan': 13, 'PHE:plan': 46, 'GLU:plan': 51, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 1436 Time building chain proxies: 4.85, per 1000 atoms: 0.63 Number of scatterers: 7747 At special positions: 0 Unit cell: (113.212, 96.778, 142.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 1440 8.00 N 1468 7.00 C 4834 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: 3.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 68.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'G' and resid 26 through 52 removed outlier: 3.662A pdb=" N ALA G 30 " --> pdb=" O CYS G 26 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 71 through 98 removed outlier: 4.272A pdb=" N VAL G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 130 removed outlier: 3.755A pdb=" N MET G 112 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 135 Processing helix chain 'G' and resid 136 through 160 Processing helix chain 'G' and resid 166 through 194 removed outlier: 4.071A pdb=" N CYS G 170 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 231 through 241 removed outlier: 4.321A pdb=" N ALA G 235 " --> pdb=" O TRP G 231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE G 236 " --> pdb=" O TRP G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'G' and resid 258 through 276 Processing helix chain 'G' and resid 284 through 329 removed outlier: 5.731A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Proline residue: G 317 - end of helix Processing helix chain 'G' and resid 347 through 352 Processing helix chain 'G' and resid 355 through 400 removed outlier: 4.588A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 435 Processing helix chain 'G' and resid 436 through 457 Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 466 through 469 Processing helix chain 'G' and resid 470 through 505 removed outlier: 3.507A pdb=" N GLN G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY G 505 " --> pdb=" O GLU G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 512 Processing helix chain 'G' and resid 515 through 548 removed outlier: 4.080A pdb=" N SER G 543 " --> pdb=" O TYR G 539 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 564 removed outlier: 3.515A pdb=" N ALA G 553 " --> pdb=" O ALA G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 615 Proline residue: G 589 - end of helix removed outlier: 4.295A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER G 615 " --> pdb=" O SER G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 727 Processing helix chain 'G' and resid 785 through 790 Processing helix chain 'G' and resid 795 through 806 removed outlier: 3.530A pdb=" N TYR G 799 " --> pdb=" O ASN G 795 " (cutoff:3.500A) Processing helix chain 'G' and resid 808 through 815 Processing helix chain 'G' and resid 831 through 846 removed outlier: 4.056A pdb=" N GLN G 846 " --> pdb=" O ARG G 842 " (cutoff:3.500A) Processing helix chain 'G' and resid 862 through 881 removed outlier: 3.755A pdb=" N LYS G 881 " --> pdb=" O LEU G 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.885A pdb=" N PHE G 917 " --> pdb=" O THR G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 927 removed outlier: 3.842A pdb=" N GLU G 926 " --> pdb=" O CYS G 922 " (cutoff:3.500A) Processing helix chain 'G' and resid 996 through 1009 removed outlier: 3.513A pdb=" N GLY G1009 " --> pdb=" O LEU G1005 " (cutoff:3.500A) Processing helix chain 'G' and resid 1009 through 1041 removed outlier: 4.376A pdb=" N LEU G1015 " --> pdb=" O LEU G1011 " (cutoff:3.500A) Processing helix chain 'G' and resid 1070 through 1107 Processing helix chain 'G' and resid 1109 through 1116 removed outlier: 3.974A pdb=" N PHE G1113 " --> pdb=" O PRO G1109 " (cutoff:3.500A) Processing helix chain 'G' and resid 1117 through 1135 removed outlier: 3.796A pdb=" N ILE G1121 " --> pdb=" O PRO G1117 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP G1128 " --> pdb=" O ARG G1124 " (cutoff:3.500A) Processing helix chain 'G' and resid 1135 through 1161 removed outlier: 3.707A pdb=" N THR G1139 " --> pdb=" O HIS G1135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G1148 " --> pdb=" O SER G1144 " (cutoff:3.500A) Processing helix chain 'G' and resid 1164 through 1210 Proline residue: G1170 - end of helix removed outlier: 4.003A pdb=" N ASP G1188 " --> pdb=" O VAL G1184 " (cutoff:3.500A) Proline residue: G1199 - end of helix removed outlier: 3.614A pdb=" N GLY G1210 " --> pdb=" O GLU G1206 " (cutoff:3.500A) Processing helix chain 'G' and resid 1210 through 1218 removed outlier: 3.678A pdb=" N ILE G1214 " --> pdb=" O GLY G1210 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1273 removed outlier: 4.025A pdb=" N PHE G1223 " --> pdb=" O TYR G1219 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA G1237 " --> pdb=" O SER G1233 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS G1273 " --> pdb=" O SER G1269 " (cutoff:3.500A) Processing helix chain 'G' and resid 1278 through 1321 removed outlier: 3.625A pdb=" N SER G1292 " --> pdb=" O ALA G1288 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN G1293 " --> pdb=" O LEU G1289 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G1314 " --> pdb=" O GLY G1310 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR G1321 " --> pdb=" O ALA G1317 " (cutoff:3.500A) Processing helix chain 'G' and resid 1385 through 1392 Processing helix chain 'G' and resid 1414 through 1421 removed outlier: 3.855A pdb=" N ARG G1421 " --> pdb=" O THR G1417 " (cutoff:3.500A) Processing helix chain 'G' and resid 1435 through 1441 Processing helix chain 'G' and resid 1447 through 1458 removed outlier: 3.668A pdb=" N LEU G1451 " --> pdb=" O SER G1447 " (cutoff:3.500A) Processing helix chain 'G' and resid 1460 through 1465 Processing helix chain 'G' and resid 1484 through 1498 removed outlier: 4.240A pdb=" N GLN G1488 " --> pdb=" O GLN G1484 " (cutoff:3.500A) Processing helix chain 'G' and resid 1512 through 1530 Processing helix chain 'G' and resid 1539 through 1543 Processing helix chain 'G' and resid 1564 through 1570 removed outlier: 3.832A pdb=" N SER G1568 " --> pdb=" O GLU G1564 " (cutoff:3.500A) Processing helix chain 'G' and resid 1571 through 1576 Processing sheet with id=AA1, first strand: chain 'G' and resid 701 through 703 Processing sheet with id=AA2, first strand: chain 'G' and resid 696 through 697 Processing sheet with id=AA3, first strand: chain 'G' and resid 850 through 854 removed outlier: 6.514A pdb=" N VAL G 851 " --> pdb=" O VAL G 885 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 887 " --> pdb=" O VAL G 851 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU G 853 " --> pdb=" O VAL G 887 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE G 901 " --> pdb=" O LEU G 708 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET G 710 " --> pdb=" O ILE G 901 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N MET G 903 " --> pdb=" O MET G 710 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL G 712 " --> pdb=" O MET G 903 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA G 902 " --> pdb=" O GLN G 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 1347 through 1348 Processing sheet with id=AA5, first strand: chain 'G' and resid 1352 through 1353 removed outlier: 3.805A pdb=" N ASP G1397 " --> pdb=" O ARG G1353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 1549 through 1551 693 hydrogen bonds defined for protein. 2037 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: 3.10 Time building geometry restraints manager: 3.76 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: 2166 1.33 - 1.45: 1399 1.45 - 1.56: 4312 1.56 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 7883 Sorted by residual: bond pdb=" CB TRP G 75 " pdb=" CG TRP G 75 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.26e+00 bond pdb=" CB TRP G 778 " pdb=" CG TRP G 778 " ideal model delta sigma weight residual 1.498 1.414 0.084 3.10e-02 1.04e+03 7.33e+00 bond pdb=" CB TRP G 231 " pdb=" CG TRP G 231 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.14e+00 bond pdb=" CA TYR G1287 " pdb=" C TYR G1287 " ideal model delta sigma weight residual 1.522 1.488 0.033 1.37e-02 5.33e+03 5.97e+00 bond pdb=" CB VAL G 596 " pdb=" CG2 VAL G 596 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.82e+00 ... (remaining 7878 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.26: 300 107.26 - 113.97: 4246 113.97 - 120.69: 3601 120.69 - 127.40: 2693 127.40 - 134.11: 93 Bond angle restraints: 10933 Sorted by residual: angle pdb=" N LEU G 104 " pdb=" CA LEU G 104 " pdb=" C LEU G 104 " ideal model delta sigma weight residual 111.54 120.73 -9.19 1.36e+00 5.41e-01 4.57e+01 angle pdb=" N GLY G 97 " pdb=" CA GLY G 97 " pdb=" C GLY G 97 " ideal model delta sigma weight residual 113.86 123.25 -9.39 1.50e+00 4.44e-01 3.92e+01 angle pdb=" N GLY G 316 " pdb=" CA GLY G 316 " pdb=" C GLY G 316 " ideal model delta sigma weight residual 112.34 124.86 -12.52 2.04e+00 2.40e-01 3.77e+01 angle pdb=" C ARG G 102 " pdb=" N HIS G 103 " pdb=" CA HIS G 103 " ideal model delta sigma weight residual 121.70 132.56 -10.86 1.80e+00 3.09e-01 3.64e+01 angle pdb=" CA ARG G 370 " pdb=" CB ARG G 370 " pdb=" CG ARG G 370 " ideal model delta sigma weight residual 114.10 102.33 11.77 2.00e+00 2.50e-01 3.46e+01 ... (remaining 10928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 4349 13.87 - 27.74: 130 27.74 - 41.61: 19 41.61 - 55.48: 4 55.48 - 69.35: 2 Dihedral angle restraints: 4504 sinusoidal: 568 harmonic: 3936 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 -137.28 -42.72 0 5.00e+00 4.00e-02 7.30e+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 93.00 143.56 -50.56 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CA ARG G 102 " pdb=" C ARG G 102 " pdb=" N HIS G 103 " pdb=" CA HIS G 103 " ideal model delta harmonic sigma weight residual 0.00 -28.18 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 4501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1114 0.074 - 0.149: 203 0.149 - 0.223: 24 0.223 - 0.297: 8 0.297 - 0.372: 2 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA PHE G 79 " pdb=" N PHE G 79 " pdb=" C PHE G 79 " pdb=" CB PHE G 79 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ARG G 370 " pdb=" N ARG G 370 " pdb=" C ARG G 370 " pdb=" CB ARG G 370 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA PHE G 295 " pdb=" N PHE G 295 " pdb=" C PHE G 295 " pdb=" CB PHE G 295 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1348 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G1286 " 0.046 2.00e-02 2.50e+03 9.17e-02 8.41e+01 pdb=" C THR G1286 " -0.159 2.00e-02 2.50e+03 pdb=" O THR G1286 " 0.058 2.00e-02 2.50e+03 pdb=" N TYR G1287 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 297 " -0.041 2.00e-02 2.50e+03 8.10e-02 6.56e+01 pdb=" C ARG G 297 " 0.140 2.00e-02 2.50e+03 pdb=" O ARG G 297 " -0.052 2.00e-02 2.50e+03 pdb=" N ARG G 298 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G1283 " -0.028 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C LEU G1283 " 0.098 2.00e-02 2.50e+03 pdb=" O LEU G1283 " -0.037 2.00e-02 2.50e+03 pdb=" N GLY G1284 " -0.033 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1763 2.76 - 3.30: 7690 3.30 - 3.83: 12664 3.83 - 4.37: 12260 4.37 - 4.90: 20825 Nonbonded interactions: 55202 Sorted by model distance: nonbonded pdb=" OG1 THR G 371 " pdb=" OH TYR G1254 " model vdw 2.231 2.440 nonbonded pdb=" O ALA G 484 " pdb=" OG1 THR G 488 " model vdw 2.258 2.440 nonbonded pdb=" O GLU G 791 " pdb=" OH TYR G1219 " model vdw 2.285 2.440 nonbonded pdb=" O TRP G 778 " pdb=" NH2 ARG G 842 " model vdw 2.330 2.520 nonbonded pdb=" O THR G 789 " pdb=" OG SER G 792 " model vdw 2.354 2.440 ... (remaining 55197 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: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.280 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.009 0.098 7883 Z= 0.613 Angle : 1.243 12.636 10933 Z= 0.756 Chirality : 0.061 0.372 1351 Planarity : 0.012 0.092 1508 Dihedral : 8.371 69.349 1933 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: -3.87 (0.18), residues: 1333 helix: -1.89 (0.13), residues: 886 sheet: -3.83 (0.50), residues: 61 loop : -3.62 (0.26), residues: 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1352 time to fit residues: 17.4074 Evaluate side-chains 57 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 122 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 HIS ** G 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 HIS ** G 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7883 Z= 0.252 Angle : 0.631 7.680 10933 Z= 0.362 Chirality : 0.042 0.168 1351 Planarity : 0.005 0.059 1508 Dihedral : 4.965 40.737 1381 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.38 % Allowed : 3.80 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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 (0.22), residues: 1333 helix: 0.52 (0.16), residues: 897 sheet: -3.78 (0.55), residues: 54 loop : -3.06 (0.28), residues: 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.930 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1211 time to fit residues: 13.4275 Evaluate side-chains 54 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 40.0000 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7883 Z= 0.179 Angle : 0.536 6.669 10933 Z= 0.298 Chirality : 0.041 0.145 1351 Planarity : 0.004 0.047 1508 Dihedral : 4.367 34.104 1381 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.37 (0.24), residues: 1333 helix: 1.60 (0.17), residues: 905 sheet: -3.22 (0.59), residues: 61 loop : -2.69 (0.30), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.939 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1161 time to fit residues: 12.5246 Evaluate side-chains 53 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 50.0000 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 50.0000 chunk 130 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7883 Z= 0.201 Angle : 0.545 6.613 10933 Z= 0.304 Chirality : 0.041 0.138 1351 Planarity : 0.004 0.047 1508 Dihedral : 4.283 34.620 1381 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.76 (0.24), residues: 1333 helix: 1.93 (0.17), residues: 897 sheet: -3.45 (0.59), residues: 54 loop : -2.52 (0.30), residues: 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.906 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1099 time to fit residues: 11.2911 Evaluate side-chains 52 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 0.2980 chunk 1 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 66 optimal weight: 40.0000 chunk 117 optimal weight: 50.0000 chunk 32 optimal weight: 30.0000 overall best weight: 8.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7883 Z= 0.267 Angle : 0.597 7.618 10933 Z= 0.343 Chirality : 0.042 0.157 1351 Planarity : 0.005 0.049 1508 Dihedral : 4.574 33.987 1381 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.55 (0.24), residues: 1333 helix: 1.73 (0.17), residues: 891 sheet: -3.41 (0.58), residues: 53 loop : -2.41 (0.30), residues: 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1086 time to fit residues: 11.3656 Evaluate side-chains 50 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7883 Z= 0.219 Angle : 0.556 6.652 10933 Z= 0.312 Chirality : 0.042 0.149 1351 Planarity : 0.004 0.047 1508 Dihedral : 4.396 34.125 1381 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.76 (0.24), residues: 1333 helix: 1.92 (0.17), residues: 900 sheet: -3.66 (0.51), residues: 59 loop : -2.44 (0.30), residues: 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1122 time to fit residues: 11.0512 Evaluate side-chains 50 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 8.9990 chunk 74 optimal weight: 0.0040 chunk 95 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 0.0170 chunk 79 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 50.0000 overall best weight: 4.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7883 Z= 0.168 Angle : 0.517 6.801 10933 Z= 0.285 Chirality : 0.041 0.144 1351 Planarity : 0.004 0.047 1508 Dihedral : 4.095 32.104 1381 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1333 helix: 2.28 (0.17), residues: 910 sheet: -3.81 (0.48), residues: 59 loop : -2.44 (0.31), residues: 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.908 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1053 time to fit residues: 11.1981 Evaluate side-chains 51 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7883 Z= 0.235 Angle : 0.563 6.765 10933 Z= 0.319 Chirality : 0.042 0.143 1351 Planarity : 0.004 0.048 1508 Dihedral : 4.298 32.552 1381 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1333 helix: 2.08 (0.17), residues: 899 sheet: -3.84 (0.48), residues: 59 loop : -2.37 (0.31), residues: 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1129 time to fit residues: 11.0140 Evaluate side-chains 48 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 124 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 120 optimal weight: 0.0970 chunk 79 optimal weight: 50.0000 overall best weight: 2.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7883 Z= 0.134 Angle : 0.500 6.860 10933 Z= 0.271 Chirality : 0.041 0.127 1351 Planarity : 0.004 0.045 1508 Dihedral : 3.933 30.782 1381 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.61 (0.25), residues: 1333 helix: 2.62 (0.17), residues: 903 sheet: -3.37 (0.51), residues: 65 loop : -2.28 (0.31), residues: 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.928 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1017 time to fit residues: 10.9226 Evaluate side-chains 50 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 134 optimal weight: 40.0000 chunk 123 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 40.0000 chunk 85 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7883 Z= 0.197 Angle : 0.543 6.715 10933 Z= 0.303 Chirality : 0.042 0.148 1351 Planarity : 0.004 0.045 1508 Dihedral : 4.067 30.761 1381 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.42 (0.24), residues: 1333 helix: 2.47 (0.17), residues: 902 sheet: -3.70 (0.51), residues: 59 loop : -2.30 (0.31), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1057 time to fit residues: 10.8671 Evaluate side-chains 49 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 94 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 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 = 0.3297 r_free = 0.3297 target = 0.068824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056683 restraints weight = 56996.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057556 restraints weight = 42099.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058106 restraints weight = 32871.779| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7883 Z= 0.272 Angle : 0.600 6.754 10933 Z= 0.345 Chirality : 0.043 0.154 1351 Planarity : 0.004 0.047 1508 Dihedral : 4.476 32.138 1381 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.88 (0.24), residues: 1333 helix: 2.01 (0.17), residues: 890 sheet: -3.62 (0.61), residues: 48 loop : -2.33 (0.30), residues: 395 =============================================================================== Job complete usr+sys time: 1124.50 seconds wall clock time: 21 minutes 16.46 seconds (1276.46 seconds total)