Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 23:39:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_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_29657/08_2023/8g0l_29657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_2023/8g0l_29657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/08_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-1.21rc1-5044/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: 26 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: 4.73, per 1000 atoms: 0.53 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 1.4 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: 1.74 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: 2.88 Time building geometry restraints manager: 4.01 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: 4715 17.89 - 35.79: 592 35.79 - 53.68: 158 53.68 - 71.57: 27 71.57 - 89.46: 11 Dihedral angle restraints: 5503 sinusoidal: 2295 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 5500 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: 1.070 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: 6.190 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.730 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- 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 : 16.919 89.463 3425 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 % 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 *********************** 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 : 1.178 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1784 time to fit residues: 11.7236 Evaluate side-chains 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1038 time to fit residues: 1.5881 ------------------------------------------------------------------------------- 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** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.0484 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= 0.231 Angle : 0.449 5.748 12214 Z= 0.228 Chirality : 0.035 0.221 1350 Planarity : 0.003 0.027 1555 Dihedral : 4.026 54.676 1198 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.44 % 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: 3.31 (0.27), residues: 1074 helix: 3.45 (0.19), residues: 749 sheet: -0.69 (1.34), residues: 16 loop : -1.06 (0.35), residues: 309 *********************** 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 51 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 1.077 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 0.1888 time to fit residues: 15.2300 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0837 time to fit residues: 2.1815 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8955 moved from start: 0.0398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9051 Z= 0.116 Angle : 0.402 8.403 12214 Z= 0.203 Chirality : 0.033 0.127 1350 Planarity : 0.003 0.029 1555 Dihedral : 3.929 52.591 1198 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.23 % 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: 3.41 (0.19), residues: 749 sheet: -1.00 (0.81), residues: 38 loop : -0.82 (0.36), residues: 287 *********************** 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 50 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 1.089 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.1709 time to fit residues: 13.2252 Evaluate side-chains 44 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0997 time to fit residues: 2.5541 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9051 Z= 0.188 Angle : 0.430 7.545 12214 Z= 0.215 Chirality : 0.034 0.124 1350 Planarity : 0.003 0.029 1555 Dihedral : 3.888 53.272 1198 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.13 % 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: -1.11 (0.89), residues: 30 loop : -0.92 (0.35), residues: 294 *********************** 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: 11 poor density : 37 time to evaluate : 1.156 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 45 average time/residue: 0.2147 time to fit residues: 14.9796 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 1.9479 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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: 0.8988 moved from start: 0.0669 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= 0.207 Angle : 0.442 6.829 12214 Z= 0.222 Chirality : 0.034 0.124 1350 Planarity : 0.003 0.029 1555 Dihedral : 3.923 53.519 1198 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.54 % 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: 3.47 (0.19), residues: 743 sheet: -0.59 (1.37), residues: 16 loop : -0.89 (0.34), residues: 315 *********************** 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 53 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 1.052 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 50 average time/residue: 0.2078 time to fit residues: 15.8485 Evaluate side-chains 44 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1664 time to fit residues: 3.1539 ------------------------------------------------------------------------------- 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: 0.0370 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0588 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= 0.116 Angle : 0.425 8.039 12214 Z= 0.210 Chirality : 0.034 0.123 1350 Planarity : 0.003 0.030 1555 Dihedral : 3.875 53.174 1198 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.51 % 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: 3.40 (0.27), residues: 1074 helix: 3.44 (0.19), residues: 744 sheet: -0.32 (1.14), residues: 24 loop : -0.74 (0.35), residues: 306 *********************** 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 44 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.221 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 0.2136 time to fit residues: 15.1305 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1182 time to fit residues: 1.8639 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8960 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9051 Z= 0.144 Angle : 0.432 6.415 12214 Z= 0.215 Chirality : 0.035 0.339 1350 Planarity : 0.003 0.031 1555 Dihedral : 3.839 53.964 1198 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.41 % 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: 3.35 (0.27), residues: 1074 helix: 3.40 (0.19), residues: 746 sheet: -0.88 (0.75), residues: 46 loop : -0.69 (0.37), residues: 282 *********************** 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 45 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.1954 time to fit residues: 13.5686 Evaluate side-chains 42 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1081 time to fit residues: 1.6389 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8976 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9051 Z= 0.191 Angle : 0.470 11.870 12214 Z= 0.229 Chirality : 0.034 0.123 1350 Planarity : 0.003 0.030 1555 Dihedral : 3.869 54.825 1198 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.10 % 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: 3.44 (0.19), residues: 745 sheet: -1.10 (0.81), residues: 38 loop : -0.79 (0.36), residues: 291 *********************** 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 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.106 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1786 time to fit residues: 11.4017 Evaluate side-chains 37 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4892 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9051 Z= 0.126 Angle : 0.456 9.420 12214 Z= 0.221 Chirality : 0.034 0.168 1350 Planarity : 0.003 0.031 1555 Dihedral : 3.858 54.774 1198 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.41 % 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: 3.35 (0.27), residues: 1074 helix: 3.40 (0.19), residues: 744 sheet: -0.40 (1.12), residues: 24 loop : -0.74 (0.35), residues: 306 *********************** 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 44 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 1.148 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1757 time to fit residues: 11.8358 Evaluate side-chains 42 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0992 time to fit residues: 1.6791 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8954 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9051 Z= 0.142 Angle : 0.471 11.716 12214 Z= 0.225 Chirality : 0.034 0.219 1350 Planarity : 0.003 0.031 1555 Dihedral : 3.840 55.572 1198 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 3.35 (0.27), residues: 1074 helix: 3.41 (0.19), residues: 745 sheet: -0.41 (1.12), residues: 24 loop : -0.77 (0.35), residues: 305 ********************** 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 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1819 time to fit residues: 11.6994 Evaluate side-chains 39 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6017 ------------------------------------------------------------------------------- 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: 6.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.025775 restraints weight = 55254.044| |-----------------------------------------------------------------------------| r_work (start): 0.2435 rms_B_bonded: 4.77 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9051 Z= 0.119 Angle : 0.464 9.851 12214 Z= 0.221 Chirality : 0.034 0.235 1350 Planarity : 0.003 0.031 1555 Dihedral : 3.840 56.053 1198 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.10 % 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: 3.31 (0.27), residues: 1074 helix: 3.37 (0.19), residues: 745 sheet: -0.42 (1.12), residues: 24 loop : -0.78 (0.35), residues: 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.48 seconds wall clock time: 28 minutes 36.22 seconds (1716.22 seconds total)