Starting phenix.real_space_refine (version: dev) on Thu May 12 20:37:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/05_2022/6pzi_20535_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/05_2022/6pzi_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_20535/05_2022/6pzi_20535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/05_2022/6pzi_20535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/05_2022/6pzi_20535_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/05_2022/6pzi_20535_neut_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'undetermined': 1, 'peptide': 1412} 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: 5.38, per 1000 atoms: 0.67 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 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: 2.11 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: 2.89 Time building geometry restraints manager: 3.65 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 - 14.11: 4489 14.11 - 28.23: 118 28.23 - 42.34: 10 42.34 - 56.45: 3 56.45 - 70.56: 1 Dihedral angle restraints: 4621 sinusoidal: 512 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 4618 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 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. 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: 0.210 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: 1.950 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 26.170 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 7.873 70.563 1944 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 % 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 *********************** 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 : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1746 time to fit residues: 15.6521 Evaluate side-chains 52 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1785 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.0178 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8141 Z= 0.153 Angle : 0.535 8.682 11333 Z= 0.291 Chirality : 0.040 0.136 1388 Planarity : 0.005 0.054 1573 Dihedral : 4.354 17.495 1447 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % 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: -0.89 (0.22), residues: 1400 helix: 0.63 (0.16), residues: 916 sheet: -3.12 (0.58), residues: 60 loop : -2.94 (0.28), residues: 424 *********************** 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 : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1168 time to fit residues: 11.6034 Evaluate side-chains 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1658 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 8141 Z= 0.311 Angle : 0.606 6.592 11333 Z= 0.353 Chirality : 0.042 0.146 1388 Planarity : 0.005 0.046 1573 Dihedral : 4.417 34.173 1447 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.42 % 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: 0.45 (0.23), residues: 1400 helix: 1.78 (0.17), residues: 916 sheet: -2.41 (0.74), residues: 51 loop : -2.76 (0.27), residues: 433 *********************** 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 53 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1216 time to fit residues: 11.3773 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1041 time to fit residues: 1.3765 ------------------------------------------------------------------------------- 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: 30.0000 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 817 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8141 Z= 0.268 Angle : 0.565 6.623 11333 Z= 0.326 Chirality : 0.041 0.144 1388 Planarity : 0.004 0.046 1573 Dihedral : 4.470 46.206 1447 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.00 % 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: 1.01 (0.23), residues: 1400 helix: 2.19 (0.17), residues: 921 sheet: -2.37 (0.67), residues: 58 loop : -2.53 (0.28), residues: 421 *********************** 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 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.917 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1108 time to fit residues: 10.0139 Evaluate side-chains 45 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1958 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 0.0870 chunk 1 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 122 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 overall best weight: 3.0362 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8141 Z= 0.176 Angle : 0.502 6.303 11333 Z= 0.274 Chirality : 0.040 0.145 1388 Planarity : 0.004 0.044 1573 Dihedral : 4.120 42.351 1447 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % 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: 1.71 (0.24), residues: 1400 helix: 2.73 (0.17), residues: 920 sheet: -2.16 (0.73), residues: 53 loop : -2.23 (0.30), residues: 427 *********************** 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 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.948 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0999 time to fit residues: 9.8173 Evaluate side-chains 46 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2083 ------------------------------------------------------------------------------- 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: 20.0000 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 491 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3610 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= 0.357 Angle : 0.633 7.817 11333 Z= 0.374 Chirality : 0.043 0.146 1388 Planarity : 0.005 0.053 1573 Dihedral : 4.656 30.278 1447 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 0.00 % 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: 0.79 (0.23), residues: 1400 helix: 1.95 (0.17), residues: 922 sheet: -2.58 (0.68), residues: 55 loop : -2.42 (0.29), residues: 423 *********************** 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 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.971 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0908 time to fit residues: 8.8057 Evaluate side-chains 46 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1769 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 0.0050 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8141 Z= 0.238 Angle : 0.544 6.357 11333 Z= 0.307 Chirality : 0.041 0.145 1388 Planarity : 0.004 0.049 1573 Dihedral : 4.336 29.215 1447 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.00 % 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: 1.32 (0.23), residues: 1400 helix: 2.41 (0.17), residues: 919 sheet: -2.18 (0.78), residues: 45 loop : -2.36 (0.28), residues: 436 *********************** 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 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.922 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0898 time to fit residues: 8.7079 Evaluate side-chains 46 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2609 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 123 optimal weight: 50.0000 chunk 130 optimal weight: 40.0000 chunk 118 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8141 Z= 0.300 Angle : 0.584 6.422 11333 Z= 0.338 Chirality : 0.041 0.141 1388 Planarity : 0.004 0.051 1573 Dihedral : 4.487 28.107 1447 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.00 % 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: 1.05 (0.23), residues: 1400 helix: 2.19 (0.17), residues: 918 sheet: -2.04 (0.80), residues: 45 loop : -2.44 (0.27), residues: 437 *********************** 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 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.949 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1126 time to fit residues: 10.3405 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2384 ------------------------------------------------------------------------------- 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: 8.9990 chunk 130 optimal weight: 50.0000 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 81 optimal weight: 40.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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: 0.8166 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8141 Z= 0.220 Angle : 0.535 7.363 11333 Z= 0.298 Chirality : 0.041 0.147 1388 Planarity : 0.004 0.048 1573 Dihedral : 4.275 27.883 1447 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.00 % 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: 1.53 (0.23), residues: 1400 helix: 2.55 (0.17), residues: 914 sheet: -1.40 (0.95), residues: 39 loop : -2.25 (0.27), residues: 447 *********************** 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 : 0.965 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1271 time to fit residues: 10.9500 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1938 ------------------------------------------------------------------------------- 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: 20.0000 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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: 0.8201 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8141 Z= 0.305 Angle : 0.592 6.550 11333 Z= 0.343 Chirality : 0.042 0.146 1388 Planarity : 0.004 0.050 1573 Dihedral : 4.547 27.663 1447 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.00 % 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: 1.03 (0.23), residues: 1400 helix: 2.22 (0.17), residues: 906 sheet: -1.78 (0.90), residues: 42 loop : -2.47 (0.27), residues: 452 ********************** 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 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1113 time to fit residues: 9.8978 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1650 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 115 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.2812 r_free = 0.2812 target = 0.037743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032034 restraints weight = 99577.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032575 restraints weight = 69252.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033018 restraints weight = 52248.273| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4128 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= 0.161 Angle : 0.507 8.730 11333 Z= 0.273 Chirality : 0.040 0.151 1388 Planarity : 0.003 0.046 1573 Dihedral : 4.140 28.026 1447 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.00 % 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: 1.88 (0.23), residues: 1400 helix: 2.89 (0.17), residues: 915 sheet: -1.42 (0.94), residues: 41 loop : -2.26 (0.27), residues: 444 =============================================================================== Job complete usr+sys time: 1152.26 seconds wall clock time: 21 minutes 34.41 seconds (1294.41 seconds total)