Starting phenix.real_space_refine on Thu Feb 13 00:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_22258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_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/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_22258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_22258.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_22258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmg_22258/02_2025/6xmg_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-5592/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: 5.19, per 1000 atoms: 0.62 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: 2.12 Conformation dependent library (CDL) restraints added in 736.6 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: 3.49 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: 3.55 Time building geometry restraints manager: 2.46 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.671 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: 0.2955 time to fit residues: 12.2920 Evaluate side-chains 27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.050103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.040617 restraints weight = 130937.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041378 restraints weight = 104933.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.041878 restraints weight = 88922.947| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8295 (t-100) cc_final: 0.7913 (t-100) REVERT: A 371 ARG cc_start: 0.9203 (tpm170) cc_final: 0.8808 (tpm170) REVERT: A 377 TYR cc_start: 0.3115 (m-10) cc_final: 0.2739 (m-10) REVERT: A 580 MET cc_start: 0.7395 (mtt) cc_final: 0.6954 (mtt) REVERT: A 631 ASP cc_start: 0.9064 (m-30) cc_final: 0.8592 (p0) REVERT: A 683 ARG cc_start: 0.9640 (mmp80) cc_final: 0.9332 (mmp80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.3504 time to fit residues: 14.3703 Evaluate side-chains 29 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.047937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.038750 restraints weight = 135069.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.039510 restraints weight = 106828.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.039993 restraints weight = 89992.001| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8861 Z= 0.221 Angle : 0.662 6.152 12714 Z= 0.340 Chirality : 0.037 0.209 1498 Planarity : 0.005 0.038 1088 Dihedral : 23.889 176.410 3081 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % 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: -1.68 (0.32), residues: 628 helix: 0.07 (0.30), residues: 284 sheet: -2.97 (0.85), residues: 30 loop : -2.09 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 724 HIS 0.007 0.001 HIS A 572 PHE 0.016 0.002 PHE A 102 TYR 0.016 0.002 TYR A 175 ARG 0.006 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 to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8329 (t-100) cc_final: 0.8102 (t-100) REVERT: A 371 ARG cc_start: 0.9364 (tpm170) cc_final: 0.8993 (tpm170) REVERT: A 377 TYR cc_start: 0.3703 (m-10) cc_final: 0.3107 (m-80) REVERT: A 631 ASP cc_start: 0.9046 (m-30) cc_final: 0.8470 (p0) REVERT: A 683 ARG cc_start: 0.9660 (mmp80) cc_final: 0.9431 (mmp80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3767 time to fit residues: 13.9700 Evaluate side-chains 26 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 20.0000 chunk 18 optimal weight: 0.4980 chunk 22 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.0670 chunk 43 optimal weight: 0.0980 chunk 29 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 overall best weight: 3.5322 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.048412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.039019 restraints weight = 130709.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.039773 restraints weight = 103606.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.040255 restraints weight = 87469.889| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3609 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= 0.182 Angle : 0.641 7.281 12714 Z= 0.326 Chirality : 0.037 0.265 1498 Planarity : 0.005 0.047 1088 Dihedral : 23.874 176.037 3081 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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: -1.50 (0.33), residues: 628 helix: 0.44 (0.31), residues: 275 sheet: -2.76 (0.89), residues: 29 loop : -2.18 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 82 HIS 0.005 0.001 HIS A 572 PHE 0.018 0.002 PHE A 533 TYR 0.015 0.002 TYR A 175 ARG 0.007 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 to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8275 (t-100) cc_final: 0.8069 (t-100) REVERT: A 579 LYS cc_start: 0.5715 (mttt) cc_final: 0.5170 (mttt) REVERT: A 628 MET cc_start: -0.1638 (ttt) cc_final: -0.4578 (ttt) REVERT: A 631 ASP cc_start: 0.9025 (m-30) cc_final: 0.8404 (p0) REVERT: A 683 ARG cc_start: 0.9654 (mmp80) cc_final: 0.9449 (mmp80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3973 time to fit residues: 14.6832 Evaluate side-chains 23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.045152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.035667 restraints weight = 133510.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036406 restraints weight = 105032.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036985 restraints weight = 88326.808| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 8861 Z= 0.275 Angle : 0.750 8.686 12714 Z= 0.380 Chirality : 0.040 0.266 1498 Planarity : 0.006 0.045 1088 Dihedral : 24.241 176.819 3081 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % 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: -1.84 (0.32), residues: 628 helix: 0.18 (0.31), residues: 278 sheet: -3.05 (0.88), residues: 30 loop : -2.41 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 82 HIS 0.005 0.001 HIS A 442 PHE 0.015 0.003 PHE A 679 TYR 0.017 0.002 TYR A 175 ARG 0.007 0.001 ARG A 675 *********************** 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 26 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8286 (t-100) cc_final: 0.8073 (t-100) REVERT: A 177 ARG cc_start: 0.8930 (mpt180) cc_final: 0.8520 (mmt180) REVERT: A 377 TYR cc_start: 0.3967 (m-10) cc_final: 0.3715 (m-10) REVERT: A 628 MET cc_start: -0.1406 (ttt) cc_final: -0.4621 (ttt) REVERT: A 631 ASP cc_start: 0.8869 (m-30) cc_final: 0.8172 (p0) REVERT: A 683 ARG cc_start: 0.9647 (mmp80) cc_final: 0.9442 (mmp80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3659 time to fit residues: 12.4941 Evaluate side-chains 22 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.045334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035877 restraints weight = 134153.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.036601 restraints weight = 105023.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.037192 restraints weight = 88574.448| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4944 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= 0.234 Angle : 0.702 8.664 12714 Z= 0.358 Chirality : 0.039 0.271 1498 Planarity : 0.005 0.063 1088 Dihedral : 24.309 174.981 3081 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.32), residues: 628 helix: 0.12 (0.30), residues: 278 sheet: -3.28 (0.84), residues: 30 loop : -2.39 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 82 HIS 0.006 0.002 HIS A 572 PHE 0.014 0.002 PHE A 533 TYR 0.016 0.002 TYR A 175 ARG 0.005 0.001 ARG A 674 *********************** 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 24 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 TYR cc_start: 0.3744 (m-10) cc_final: 0.3017 (m-10) REVERT: A 683 ARG cc_start: 0.9645 (mmp80) cc_final: 0.9444 (mmp80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.3665 time to fit residues: 11.5708 Evaluate side-chains 19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.046317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036729 restraints weight = 131435.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037531 restraints weight = 103237.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.038146 restraints weight = 86265.983| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8861 Z= 0.198 Angle : 0.668 8.622 12714 Z= 0.343 Chirality : 0.038 0.271 1498 Planarity : 0.005 0.049 1088 Dihedral : 24.229 174.986 3081 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -1.85 (0.32), residues: 628 helix: 0.10 (0.30), residues: 278 sheet: -3.29 (0.83), residues: 30 loop : -2.31 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 82 HIS 0.004 0.001 HIS A 572 PHE 0.018 0.002 PHE A 733 TYR 0.016 0.002 TYR A 175 ARG 0.005 0.001 ARG A 674 *********************** 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 27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 TYR cc_start: 0.3694 (m-10) cc_final: 0.3056 (m-80) REVERT: A 410 MET cc_start: 0.8693 (ptp) cc_final: 0.8471 (ptp) REVERT: A 580 MET cc_start: 0.7665 (mmt) cc_final: 0.7340 (mmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3411 time to fit residues: 12.1718 Evaluate side-chains 19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 442 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.043927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034598 restraints weight = 137663.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.035397 restraints weight = 107237.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035943 restraints weight = 89087.005| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8861 Z= 0.287 Angle : 0.777 9.167 12714 Z= 0.396 Chirality : 0.041 0.268 1498 Planarity : 0.006 0.048 1088 Dihedral : 24.504 175.557 3081 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 36.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % 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: -2.10 (0.32), residues: 628 helix: -0.12 (0.31), residues: 271 sheet: -2.99 (0.67), residues: 44 loop : -2.37 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 82 HIS 0.005 0.002 HIS A 576 PHE 0.016 0.003 PHE A 756 TYR 0.017 0.002 TYR A 175 ARG 0.012 0.001 ARG A 686 *********************** 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 25 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8486 (t-100) cc_final: 0.8089 (t-100) REVERT: A 177 ARG cc_start: 0.8492 (mpt180) cc_final: 0.8266 (mmt180) REVERT: A 410 MET cc_start: 0.9553 (ptp) cc_final: 0.9341 (ptp) REVERT: A 580 MET cc_start: 0.7330 (mmt) cc_final: 0.7085 (mmm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3633 time to fit residues: 11.7595 Evaluate side-chains 21 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 71 optimal weight: 10.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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 ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.041816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032847 restraints weight = 141784.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033603 restraints weight = 108941.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.034142 restraints weight = 90629.668| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8861 Z= 0.344 Angle : 0.869 10.478 12714 Z= 0.445 Chirality : 0.045 0.270 1498 Planarity : 0.007 0.062 1088 Dihedral : 24.954 174.075 3081 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 45.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 0.20 % Allowed : 1.21 % Favored : 98.59 % 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: -2.51 (0.32), residues: 628 helix: -0.51 (0.30), residues: 272 sheet: -3.20 (0.67), residues: 45 loop : -2.54 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 82 HIS 0.006 0.002 HIS A 442 PHE 0.022 0.003 PHE A 733 TYR 0.019 0.003 TYR A 393 ARG 0.010 0.001 ARG A 683 *********************** 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 27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.8585 (mpt180) cc_final: 0.8354 (mmt180) REVERT: A 377 TYR cc_start: 0.4408 (m-10) cc_final: 0.3789 (m-10) REVERT: A 563 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8178 (pp30) REVERT: A 580 MET cc_start: 0.7538 (mmt) cc_final: 0.6901 (mmm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.4016 time to fit residues: 13.8629 Evaluate side-chains 21 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 0.0170 chunk 10 optimal weight: 6.9990 overall best weight: 2.8020 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.045317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.035682 restraints weight = 133555.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.036547 restraints weight = 103223.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.037200 restraints weight = 84925.743| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8861 Z= 0.204 Angle : 0.730 9.220 12714 Z= 0.376 Chirality : 0.040 0.269 1498 Planarity : 0.008 0.144 1088 Dihedral : 24.667 174.119 3081 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % 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: -2.28 (0.32), residues: 628 helix: -0.41 (0.30), residues: 274 sheet: -3.23 (0.62), residues: 45 loop : -2.29 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 82 HIS 0.004 0.001 HIS A 179 PHE 0.017 0.002 PHE A 84 TYR 0.013 0.002 TYR A 175 ARG 0.021 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 27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8066 (t-100) cc_final: 0.7864 (t-100) REVERT: A 410 MET cc_start: 0.9273 (ptt) cc_final: 0.8658 (ppp) REVERT: A 580 MET cc_start: 0.7044 (mmt) cc_final: 0.6811 (mmm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.3323 time to fit residues: 11.8914 Evaluate side-chains 20 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.044921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.035400 restraints weight = 135905.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.036247 restraints weight = 104632.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.036888 restraints weight = 86179.762| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8861 Z= 0.198 Angle : 0.700 8.681 12714 Z= 0.360 Chirality : 0.039 0.264 1498 Planarity : 0.007 0.087 1088 Dihedral : 24.567 175.009 3081 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 30.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % 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: -2.12 (0.32), residues: 628 helix: -0.30 (0.30), residues: 274 sheet: -3.08 (0.65), residues: 44 loop : -2.21 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 82 HIS 0.005 0.002 HIS A 179 PHE 0.015 0.002 PHE A 533 TYR 0.017 0.002 TYR A 175 ARG 0.008 0.001 ARG A 674 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.61 seconds wall clock time: 40 minutes 24.68 seconds (2424.68 seconds total)