Starting phenix.real_space_refine on Tue Sep 24 17:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/09_2024/6xmg_22258.cif" } resolution = 4.8 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 154 5.49 5 S 11 5.16 5 C 4674 2.51 5 N 1553 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5081 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 38, 'TRANS': 599} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2772 Classifications: {'RNA': 130} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 56} Link IDs: {'rna2p': 15, 'rna3p': 114} Chain breaks: 1 Chain: "E" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 507 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4654 SG CYS A 714 51.688 83.830 49.919 1.00352.65 S Time building chain proxies: 5.34, per 1000 atoms: 0.64 Number of scatterers: 8361 At special positions: 0 Unit cell: (106.05, 94.5, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 11 16.00 P 154 15.00 O 1968 8.00 N 1553 7.00 C 4674 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 681.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 49.4% alpha, 5.8% beta 43 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.637A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.754A pdb=" N TRP A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.970A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.622A pdb=" N ARG A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.818A pdb=" N SER A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.518A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 200 removed outlier: 3.892A pdb=" N GLN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.540A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.565A pdb=" N LYS A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.669A pdb=" N THR A 434 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.741A pdb=" N LEU A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.723A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 569 through 595 removed outlier: 3.804A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 644 removed outlier: 3.593A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.660A pdb=" N ARG A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 4.009A pdb=" N ARG A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.630A pdb=" N TRP A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.685A pdb=" N ARG A 26 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 450 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 438 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 441 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.564A pdb=" N VAL A 653 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 652 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524 removed outlier: 6.725A pdb=" N ALA A 521 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 532 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 523 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 530 " --> pdb=" O PHE A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 195 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 2.58 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: 1025 1.31 - 1.43: 3323 1.43 - 1.56: 4192 1.56 - 1.69: 305 1.69 - 1.81: 16 Bond restraints: 8861 Sorted by residual: bond pdb=" C ARG A 675 " pdb=" O ARG A 675 " ideal model delta sigma weight residual 1.233 1.180 0.052 1.09e-02 8.42e+03 2.31e+01 bond pdb=" C ARG A 675 " pdb=" N VAL A 676 " ideal model delta sigma weight residual 1.332 1.305 0.026 1.36e-02 5.41e+03 3.79e+00 bond pdb=" CA ILE A 766 " pdb=" CB ILE A 766 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.68e+00 bond pdb=" N ARG A 675 " pdb=" CA ARG A 675 " ideal model delta sigma weight residual 1.463 1.482 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" N LYS A 551 " pdb=" CA LYS A 551 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 12399 1.49 - 2.98: 263 2.98 - 4.47: 40 4.47 - 5.95: 11 5.95 - 7.44: 1 Bond angle restraints: 12714 Sorted by residual: angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" CB PRO A 229 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C3' A C 113 " pdb=" O3' A C 113 " pdb=" P A C 114 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" N GLN A 552 " pdb=" CA GLN A 552 " pdb=" C GLN A 552 " ideal model delta sigma weight residual 107.73 112.27 -4.54 1.34e+00 5.57e-01 1.15e+01 angle pdb=" C LEU A 203 " pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 122.89 119.38 3.51 1.12e+00 7.97e-01 9.84e+00 angle pdb=" C LYS A 610 " pdb=" CA LYS A 610 " pdb=" CB LYS A 610 " ideal model delta sigma weight residual 110.88 115.55 -4.67 1.57e+00 4.06e-01 8.86e+00 ... (remaining 12709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5085 35.70 - 71.39: 409 71.39 - 107.09: 54 107.09 - 142.78: 4 142.78 - 178.48: 5 Dihedral angle restraints: 5557 sinusoidal: 3693 harmonic: 1864 Sorted by residual: dihedral pdb=" O4' U C 55 " pdb=" C1' U C 55 " pdb=" N1 U C 55 " pdb=" C2 U C 55 " ideal model delta sinusoidal sigma weight residual 200.00 44.85 155.15 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual 232.00 57.13 174.87 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA GLU A 21 " pdb=" C GLU A 21 " pdb=" N ARG A 22 " pdb=" CA ARG A 22 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1346 0.046 - 0.093: 128 0.093 - 0.139: 19 0.139 - 0.185: 3 0.185 - 0.232: 2 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA PRO A 229 " pdb=" N PRO A 229 " pdb=" C PRO A 229 " pdb=" CB PRO A 229 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' A C 113 " pdb=" C4' A C 113 " pdb=" O3' A C 113 " pdb=" C2' A C 113 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A C 76 " pdb=" C4' A C 76 " pdb=" O3' A C 76 " pdb=" C2' A C 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1495 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 675 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ARG A 675 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 675 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 676 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 427 " -0.014 2.00e-02 2.50e+03 1.38e-02 3.83e+00 pdb=" CG TYR A 427 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 427 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 427 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 427 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 427 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 156 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 157 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.023 5.00e-02 4.00e+02 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 658 2.73 - 3.27: 8128 3.27 - 3.81: 15463 3.81 - 4.36: 19635 4.36 - 4.90: 27945 Nonbonded interactions: 71829 Sorted by model distance: nonbonded pdb=" O CYS A 714 " pdb="ZN ZN A 801 " model vdw 2.187 2.230 nonbonded pdb=" O ARG A 685 " pdb=" OG1 THR A 689 " model vdw 2.276 3.040 nonbonded pdb=" O2' U C 13 " pdb=" OP2 G C 22 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR A 466 " pdb=" OE1 GLU A 468 " model vdw 2.293 3.040 nonbonded pdb=" NH2 ARG A 26 " pdb=" O2' C C 111 " model vdw 2.299 3.120 ... (remaining 71824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.000 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 25.820 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.002 0.052 8861 Z= 0.130 Angle : 0.526 7.443 12714 Z= 0.329 Chirality : 0.029 0.232 1498 Planarity : 0.004 0.041 1088 Dihedral : 21.640 178.481 4339 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.33), residues: 628 helix: -0.24 (0.31), residues: 275 sheet: -3.40 (0.70), residues: 40 loop : -2.07 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.002 0.001 HIS A 159 PHE 0.010 0.001 PHE A 398 TYR 0.033 0.002 TYR A 427 ARG 0.007 0.001 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8048 (t-100) cc_final: 0.7491 (t-100) REVERT: A 177 ARG cc_start: 0.8976 (mpt180) cc_final: 0.8533 (mmt180) REVERT: A 371 ARG cc_start: 0.9227 (tpm170) cc_final: 0.8842 (tpm170) REVERT: A 631 ASP cc_start: 0.8883 (m-30) cc_final: 0.8400 (p0) REVERT: A 683 ARG cc_start: 0.9657 (mmp80) cc_final: 0.9224 (mmp80) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2908 time to fit residues: 12.1056 Evaluate side-chains 27 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 115 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN A 572 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8861 Z= 0.254 Angle : 0.716 7.060 12714 Z= 0.359 Chirality : 0.039 0.209 1498 Planarity : 0.005 0.041 1088 Dihedral : 23.526 179.265 3081 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.20 % Allowed : 3.22 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 628 helix: 0.06 (0.30), residues: 280 sheet: -2.87 (0.88), residues: 30 loop : -1.95 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 724 HIS 0.002 0.001 HIS A 440 PHE 0.017 0.002 PHE A 756 TYR 0.017 0.002 TYR A 427 ARG 0.007 0.001 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8524 (t-100) cc_final: 0.8052 (t-100) REVERT: A 371 ARG cc_start: 0.9267 (tpm170) cc_final: 0.8872 (tpm170) REVERT: A 377 TYR cc_start: 0.3206 (m-10) cc_final: 0.2888 (m-10) REVERT: A 580 MET cc_start: 0.7763 (mtt) cc_final: 0.7382 (mtt) REVERT: A 631 ASP cc_start: 0.8990 (m-30) cc_final: 0.8503 (p0) REVERT: A 683 ARG cc_start: 0.9678 (mmp80) cc_final: 0.9403 (mmp80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.3495 time to fit residues: 14.4129 Evaluate side-chains 29 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 54 ASN A 115 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8861 Z= 0.247 Angle : 0.697 6.795 12714 Z= 0.357 Chirality : 0.038 0.209 1498 Planarity : 0.005 0.040 1088 Dihedral : 23.995 176.090 3081 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.32), residues: 628 helix: 0.00 (0.30), residues: 284 sheet: -2.88 (0.84), residues: 29 loop : -2.19 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 724 HIS 0.008 0.001 HIS A 572 PHE 0.019 0.003 PHE A 102 TYR 0.017 0.002 TYR A 175 ARG 0.008 0.001 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8490 (t-100) cc_final: 0.8225 (t-100) REVERT: A 371 ARG cc_start: 0.9386 (tpm170) cc_final: 0.9046 (tpm170) REVERT: A 377 TYR cc_start: 0.3651 (m-10) cc_final: 0.3241 (m-80) REVERT: A 631 ASP cc_start: 0.8884 (m-30) cc_final: 0.8269 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3960 time to fit residues: 14.3791 Evaluate side-chains 23 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 0.0980 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8861 Z= 0.163 Angle : 0.635 8.584 12714 Z= 0.322 Chirality : 0.037 0.252 1498 Planarity : 0.005 0.038 1088 Dihedral : 23.857 175.638 3081 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.33), residues: 628 helix: 0.16 (0.30), residues: 284 sheet: -2.72 (0.89), residues: 29 loop : -2.09 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.007 0.001 HIS A 624 PHE 0.015 0.002 PHE A 756 TYR 0.015 0.002 TYR A 175 ARG 0.008 0.001 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8398 (t-100) cc_final: 0.8184 (t-100) REVERT: A 628 MET cc_start: -0.1608 (ttt) cc_final: -0.4508 (ttt) REVERT: A 631 ASP cc_start: 0.8910 (m-30) cc_final: 0.8287 (p0) REVERT: A 683 ARG cc_start: 0.9733 (mmp80) cc_final: 0.9490 (mmp80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3816 time to fit residues: 14.0590 Evaluate side-chains 22 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8861 Z= 0.257 Angle : 0.722 8.916 12714 Z= 0.366 Chirality : 0.039 0.260 1498 Planarity : 0.006 0.055 1088 Dihedral : 24.127 176.943 3081 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.32), residues: 628 helix: 0.20 (0.31), residues: 278 sheet: -2.96 (0.86), residues: 29 loop : -2.37 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 82 HIS 0.004 0.001 HIS A 572 PHE 0.014 0.002 PHE A 756 TYR 0.016 0.002 TYR A 175 ARG 0.011 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.8904 (mpt180) cc_final: 0.8444 (mmt180) REVERT: A 377 TYR cc_start: 0.3829 (m-10) cc_final: 0.3285 (m-10) REVERT: A 628 MET cc_start: -0.1193 (ttt) cc_final: -0.4379 (ttt) REVERT: A 631 ASP cc_start: 0.8725 (m-30) cc_final: 0.8044 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3392 time to fit residues: 11.1637 Evaluate side-chains 20 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 30.0000 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8861 Z= 0.304 Angle : 0.790 9.129 12714 Z= 0.403 Chirality : 0.042 0.272 1498 Planarity : 0.006 0.061 1088 Dihedral : 24.537 175.312 3081 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 35.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -2.12 (0.32), residues: 628 helix: -0.15 (0.30), residues: 274 sheet: -3.31 (0.84), residues: 30 loop : -2.42 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 82 HIS 0.007 0.002 HIS A 572 PHE 0.021 0.003 PHE A 452 TYR 0.018 0.002 TYR A 175 ARG 0.009 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.709 Fit side-chains REVERT: A 170 TRP cc_start: 0.8440 (t-100) cc_final: 0.8189 (t-100) REVERT: A 177 ARG cc_start: 0.8786 (mpt180) cc_final: 0.8403 (mmt180) REVERT: A 377 TYR cc_start: 0.4471 (m-10) cc_final: 0.3996 (m-10) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3135 time to fit residues: 10.5803 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 22 optimal weight: 0.0370 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8861 Z= 0.233 Angle : 0.722 9.310 12714 Z= 0.371 Chirality : 0.040 0.272 1498 Planarity : 0.006 0.104 1088 Dihedral : 24.530 174.640 3081 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 31.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.32), residues: 628 helix: -0.06 (0.31), residues: 273 sheet: -3.01 (0.67), residues: 44 loop : -2.30 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 82 HIS 0.009 0.002 HIS A 681 PHE 0.023 0.003 PHE A 733 TYR 0.016 0.002 TYR A 175 ARG 0.012 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.9721 (mm-30) cc_final: 0.9514 (mm-30) REVERT: A 170 TRP cc_start: 0.8305 (t-100) cc_final: 0.8071 (t-100) REVERT: A 177 ARG cc_start: 0.8691 (mpt180) cc_final: 0.8350 (mmt180) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.2863 time to fit residues: 10.2911 Evaluate side-chains 21 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8861 Z= 0.224 Angle : 0.702 8.629 12714 Z= 0.361 Chirality : 0.039 0.272 1498 Planarity : 0.006 0.097 1088 Dihedral : 24.469 175.001 3081 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.33), residues: 628 helix: -0.04 (0.31), residues: 274 sheet: -3.02 (0.67), residues: 44 loop : -2.26 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 82 HIS 0.005 0.002 HIS A 572 PHE 0.015 0.002 PHE A 733 TYR 0.016 0.002 TYR A 175 ARG 0.006 0.001 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.9706 (mm-30) cc_final: 0.9502 (mm-30) REVERT: A 170 TRP cc_start: 0.8176 (t-100) cc_final: 0.7947 (t-100) REVERT: A 177 ARG cc_start: 0.8652 (mpt180) cc_final: 0.8334 (mmt180) REVERT: A 377 TYR cc_start: 0.4035 (m-10) cc_final: 0.3754 (m-10) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3308 time to fit residues: 11.5228 Evaluate side-chains 21 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 40.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 54 ASN A 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8861 Z= 0.225 Angle : 0.702 8.648 12714 Z= 0.360 Chirality : 0.039 0.269 1498 Planarity : 0.006 0.053 1088 Dihedral : 24.426 174.987 3081 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), residues: 628 helix: 0.07 (0.31), residues: 274 sheet: -3.13 (0.66), residues: 44 loop : -2.23 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 82 HIS 0.004 0.001 HIS A 681 PHE 0.015 0.002 PHE A 733 TYR 0.017 0.002 TYR A 175 ARG 0.009 0.001 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8077 (t-100) cc_final: 0.7827 (t-100) REVERT: A 177 ARG cc_start: 0.8622 (mpt180) cc_final: 0.8365 (mmt180) REVERT: A 377 TYR cc_start: 0.3972 (m-10) cc_final: 0.3722 (m-10) REVERT: A 563 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8766 (pp30) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.2622 time to fit residues: 9.2849 Evaluate side-chains 22 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8861 Z= 0.235 Angle : 0.717 8.827 12714 Z= 0.368 Chirality : 0.039 0.266 1498 Planarity : 0.006 0.067 1088 Dihedral : 24.516 174.861 3081 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 33.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.20 % Allowed : 1.01 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.33), residues: 628 helix: 0.00 (0.31), residues: 273 sheet: -3.11 (0.66), residues: 44 loop : -2.23 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 82 HIS 0.006 0.002 HIS A 576 PHE 0.015 0.002 PHE A 679 TYR 0.017 0.002 TYR A 175 ARG 0.009 0.001 ARG A 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.9710 (mm-30) cc_final: 0.9508 (tp30) REVERT: A 170 TRP cc_start: 0.8068 (t-100) cc_final: 0.7826 (t-100) REVERT: A 177 ARG cc_start: 0.8622 (mpt180) cc_final: 0.8400 (mmt180) REVERT: A 377 TYR cc_start: 0.3809 (m-10) cc_final: 0.3563 (m-10) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.2853 time to fit residues: 10.3911 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.0040 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 4.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.044646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.035360 restraints weight = 134325.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.036177 restraints weight = 104115.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.036763 restraints weight = 85938.892| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8861 Z= 0.218 Angle : 0.711 8.676 12714 Z= 0.365 Chirality : 0.039 0.264 1498 Planarity : 0.006 0.043 1088 Dihedral : 24.480 174.618 3081 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 31.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.33), residues: 628 helix: -0.10 (0.31), residues: 272 sheet: -3.15 (0.65), residues: 44 loop : -2.21 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 82 HIS 0.004 0.002 HIS A 179 PHE 0.018 0.002 PHE A 533 TYR 0.017 0.002 TYR A 175 ARG 0.008 0.001 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.54 seconds wall clock time: 24 minutes 55.36 seconds (1495.36 seconds total)