Starting phenix.real_space_refine on Fri Dec 8 17:41:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/12_2023/8g0l_29657_updated.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 48 5.16 5 C 5674 2.51 5 N 1487 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "B" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7531 Classifications: {'peptide': 925} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 891} Chain breaks: 4 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'CMC': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="MET C 5 " pdbres="CMC C 201 " Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CMC:plan-5': 1, 'CMC:plan-3': 1, 'CMC:plan-1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.03, per 1000 atoms: 0.57 Number of scatterers: 8872 At special positions: 0 Unit cell: (77.4, 111.8, 127.28, 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 48 16.00 P 1 15.00 O 1662 8.00 N 1487 7.00 C 5674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.9 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 3 sheets defined 67.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 16 through 19 No H-bonds generated for 'chain 'A' and resid 16 through 19' Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'B' and resid 10 through 23 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.860A pdb=" N LYS B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.565A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 245 through 258 Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.638A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.903A pdb=" N VAL B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 432 through 454 removed outlier: 4.297A pdb=" N GLU B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 485 through 501 removed outlier: 3.618A pdb=" N HIS B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 519 Processing helix chain 'B' and resid 523 through 532 removed outlier: 4.106A pdb=" N ASP B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.283A pdb=" N ASP B 540 " --> pdb=" O HIS B 536 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.893A pdb=" N TYR B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 553 " --> pdb=" O TYR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 587 removed outlier: 4.760A pdb=" N SER B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 607 through 623 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 649 through 651 No H-bonds generated for 'chain 'B' and resid 649 through 651' Processing helix chain 'B' and resid 673 through 703 removed outlier: 4.094A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Proline residue: B 701 - end of helix Processing helix chain 'B' and resid 723 through 747 removed outlier: 3.659A pdb=" N LYS B 747 " --> pdb=" O ARG B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 767 Processing helix chain 'B' and resid 769 through 789 Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.546A pdb=" N CYS B 819 " --> pdb=" O VAL B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 869 Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 886 through 916 Processing helix chain 'B' and resid 932 through 970 removed outlier: 3.758A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS B 969 " --> pdb=" O GLU B 965 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 970 " --> pdb=" O THR B 966 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.305A pdb=" N GLY A 55 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS A 60 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 74 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 62 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY A 72 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 108 through 113 removed outlier: 5.912A pdb=" N ARG A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 130 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 825 through 827 517 hydrogen bonds defined for protein. 1500 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: 2.94 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1483 1.31 - 1.44: 2353 1.44 - 1.57: 5135 1.57 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9051 Sorted by residual: bond pdb=" O3A CMC C 201 " pdb=" P2A CMC C 201 " ideal model delta sigma weight residual 1.674 1.510 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C2 CMC C 201 " pdb=" O21 CMC C 201 " ideal model delta sigma weight residual 1.263 1.400 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" O6A CMC C 201 " pdb=" P2A CMC C 201 " ideal model delta sigma weight residual 1.717 1.639 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5P CMC C 201 " pdb=" C6P CMC C 201 " ideal model delta sigma weight residual 1.603 1.542 0.061 2.00e-02 2.50e+03 9.24e+00 bond pdb=" C7P CMC C 201 " pdb=" N8P CMC C 201 " ideal model delta sigma weight residual 1.521 1.469 0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 9046 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 177 106.03 - 113.02: 4865 113.02 - 120.00: 3167 120.00 - 126.99: 3917 126.99 - 133.98: 88 Bond angle restraints: 12214 Sorted by residual: angle pdb=" C1 CMC C 201 " pdb=" C2 CMC C 201 " pdb=" O21 CMC C 201 " ideal model delta sigma weight residual 119.98 108.38 11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " pdb=" CG GLN A 125 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" N GLY B 346 " pdb=" CA GLY B 346 " pdb=" C GLY B 346 " ideal model delta sigma weight residual 111.85 114.78 -2.93 1.06e+00 8.90e-01 7.63e+00 ... (remaining 12209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4716 17.89 - 35.79: 592 35.79 - 53.68: 158 53.68 - 71.57: 28 71.57 - 89.46: 11 Dihedral angle restraints: 5505 sinusoidal: 2297 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLU B 128 " pdb=" C GLU B 128 " pdb=" N TYR B 129 " pdb=" CA TYR B 129 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 89.46 -89.46 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP B 43 " pdb=" CB ASP B 43 " pdb=" CG ASP B 43 " pdb=" OD1 ASP B 43 " ideal model delta sinusoidal sigma weight residual -30.00 -85.86 55.86 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 961 0.029 - 0.057: 245 0.057 - 0.086: 97 0.086 - 0.115: 43 0.115 - 0.143: 4 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE B 582 " pdb=" CA ILE B 582 " pdb=" CG1 ILE B 582 " pdb=" CG2 ILE B 582 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO B 323 " pdb=" N PRO B 323 " pdb=" C PRO B 323 " pdb=" CB PRO B 323 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE B 647 " pdb=" N ILE B 647 " pdb=" C ILE B 647 " pdb=" CB ILE B 647 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1347 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 21 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 22 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 16 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO B 17 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 758 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.015 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2497 2.81 - 3.33: 9001 3.33 - 3.86: 14543 3.86 - 4.38: 15479 4.38 - 4.90: 26929 Nonbonded interactions: 68449 Sorted by model distance: nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.289 2.440 nonbonded pdb=" O TYR B 149 " pdb=" OG SER B 152 " model vdw 2.314 2.440 nonbonded pdb=" OE1 GLN B 555 " pdb=" OG SER B 952 " model vdw 2.320 2.440 nonbonded pdb=" OD2 ASP B 484 " pdb=" OG1 THR B 486 " model vdw 2.353 2.440 nonbonded pdb=" N GLN B 61 " pdb=" OE1 GLN B 61 " model vdw 2.358 2.520 ... (remaining 68444 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 individual isotropic 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: 1.380 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: 0.000 Extract box with map and model: 5.890 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 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 : 0.003 0.164 9051 Z= 0.234 Angle : 0.485 11.598 12214 Z= 0.239 Chirality : 0.034 0.143 1350 Planarity : 0.003 0.029 1555 Dihedral : 16.945 89.463 3427 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 23.49 % Favored : 76.41 % 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: 3.32 (0.27), residues: 1074 helix: 3.43 (0.19), residues: 750 sheet: 0.10 (1.45), residues: 16 loop : -1.04 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.010 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.168 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1856 time to fit residues: 12.1242 Evaluate side-chains 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1013 time to fit residues: 1.6504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.0449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.228 Angle : 0.446 5.560 12214 Z= 0.227 Chirality : 0.035 0.230 1350 Planarity : 0.003 0.028 1555 Dihedral : 4.381 58.284 1200 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 23.08 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.27), residues: 1074 helix: 3.43 (0.19), residues: 750 sheet: -0.65 (1.34), residues: 16 loop : -1.05 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 281 HIS 0.002 0.001 HIS B 834 PHE 0.026 0.001 PHE C 4 TYR 0.016 0.001 TYR B 580 ARG 0.002 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 1.051 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 0.1893 time to fit residues: 14.4727 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0820 time to fit residues: 2.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.0060 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS B 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9051 Z= 0.200 Angle : 0.430 8.739 12214 Z= 0.218 Chirality : 0.034 0.128 1350 Planarity : 0.003 0.029 1555 Dihedral : 4.323 58.735 1200 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 22.87 % Favored : 75.49 % 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: 3.29 (0.27), residues: 1074 helix: 3.42 (0.19), residues: 749 sheet: -0.79 (1.30), residues: 16 loop : -1.01 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.011 0.001 PHE B 150 TYR 0.016 0.001 TYR B 580 ARG 0.003 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 1.037 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 49 average time/residue: 0.1736 time to fit residues: 13.9659 Evaluate side-chains 46 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1037 time to fit residues: 3.1934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.0020 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9051 Z= 0.113 Angle : 0.402 6.747 12214 Z= 0.202 Chirality : 0.034 0.123 1350 Planarity : 0.003 0.030 1555 Dihedral : 4.245 58.613 1200 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.92 % Allowed : 23.59 % Favored : 75.49 % 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: 3.35 (0.27), residues: 1074 helix: 3.46 (0.19), residues: 743 sheet: -1.18 (0.76), residues: 46 loop : -0.76 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.017 0.001 PHE A 15 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 1.148 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 46 average time/residue: 0.2184 time to fit residues: 15.4476 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0861 time to fit residues: 1.7050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9051 Z= 0.362 Angle : 0.560 8.460 12214 Z= 0.279 Chirality : 0.036 0.131 1350 Planarity : 0.003 0.028 1555 Dihedral : 4.410 55.221 1200 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.05 % Allowed : 23.79 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.27), residues: 1074 helix: 3.46 (0.19), residues: 732 sheet: -1.68 (0.98), residues: 24 loop : -0.73 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.003 0.001 HIS B 907 PHE 0.023 0.001 PHE A 15 TYR 0.015 0.001 TYR B 580 ARG 0.005 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 1.136 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 55 average time/residue: 0.2263 time to fit residues: 18.7890 Evaluate side-chains 44 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0872 time to fit residues: 2.5167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9051 Z= 0.209 Angle : 0.474 9.145 12214 Z= 0.238 Chirality : 0.035 0.222 1350 Planarity : 0.003 0.029 1555 Dihedral : 4.419 59.089 1200 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.41 % Allowed : 24.62 % Favored : 74.97 % 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: 3.30 (0.27), residues: 1074 helix: 3.45 (0.19), residues: 734 sheet: -1.72 (0.96), residues: 24 loop : -0.72 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.001 HIS B 448 PHE 0.015 0.001 PHE A 15 TYR 0.017 0.001 TYR B 580 ARG 0.003 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.188 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1764 time to fit residues: 12.3415 Evaluate side-chains 42 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0948 time to fit residues: 2.0800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9051 Z= 0.150 Angle : 0.456 12.080 12214 Z= 0.225 Chirality : 0.034 0.123 1350 Planarity : 0.003 0.031 1555 Dihedral : 4.342 59.664 1200 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.21 % Allowed : 25.03 % Favored : 74.77 % 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: 3.39 (0.27), residues: 1074 helix: 3.48 (0.19), residues: 738 sheet: -0.85 (1.31), residues: 16 loop : -0.76 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.011 0.001 PHE A 15 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.070 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1826 time to fit residues: 12.0919 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1064 time to fit residues: 1.6575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9051 Z= 0.128 Angle : 0.459 8.834 12214 Z= 0.224 Chirality : 0.035 0.329 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.304 59.289 1200 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.31 % Allowed : 24.51 % Favored : 75.18 % 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: 3.37 (0.27), residues: 1074 helix: 3.46 (0.19), residues: 737 sheet: -0.34 (1.15), residues: 24 loop : -0.74 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.009 0.001 PHE B 150 TYR 0.016 0.001 TYR B 580 ARG 0.001 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.201 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1814 time to fit residues: 12.6898 Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0803 time to fit residues: 1.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9051 Z= 0.134 Angle : 0.470 9.853 12214 Z= 0.226 Chirality : 0.035 0.296 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.308 59.761 1200 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 24.82 % Favored : 75.18 % 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: 3.37 (0.27), residues: 1074 helix: 3.45 (0.19), residues: 738 sheet: -0.32 (1.15), residues: 24 loop : -0.76 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.022 0.001 PHE C 4 TYR 0.017 0.001 TYR B 580 ARG 0.001 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1841 time to fit residues: 11.8914 Evaluate side-chains 38 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9051 Z= 0.130 Angle : 0.483 12.379 12214 Z= 0.227 Chirality : 0.034 0.197 1350 Planarity : 0.003 0.033 1555 Dihedral : 4.267 59.299 1200 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.21 % Allowed : 24.82 % Favored : 74.97 % 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: 3.33 (0.27), residues: 1074 helix: 3.39 (0.19), residues: 745 sheet: -0.29 (1.16), residues: 24 loop : -0.78 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.009 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.001 0.000 ARG B 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.089 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1810 time to fit residues: 12.2933 Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1144 time to fit residues: 1.9052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.025913 restraints weight = 55072.732| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 4.76 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9051 Z= 0.122 Angle : 0.473 10.643 12214 Z= 0.224 Chirality : 0.034 0.198 1350 Planarity : 0.003 0.033 1555 Dihedral : 4.244 59.378 1200 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 24.82 % Favored : 75.18 % 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: 3.34 (0.27), residues: 1074 helix: 3.39 (0.19), residues: 745 sheet: -0.84 (1.12), residues: 26 loop : -0.71 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 281 HIS 0.002 0.000 HIS A 73 PHE 0.008 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.001 0.000 ARG B 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1568.29 seconds wall clock time: 29 minutes 48.61 seconds (1788.61 seconds total)