Starting phenix.real_space_refine on Fri Sep 11 07:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmg_22258/09_2026/6xmg_22258.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 3, 'HIS:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2772 Classifications: {'RNAv2': 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: {'RNAv2': 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: 1.47, per 1000 atoms: 0.18 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: 0.59 Conformation dependent library (CDL) restraints added in 120.0 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: 0.95 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: 1.42 Time building geometry restraints manager: 0.77 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=" C3' A C 113 " pdb=" O3' A C 113 " ideal model delta sigma weight residual 1.415 1.444 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11992 1.49 - 2.98: 603 2.98 - 4.47: 89 4.47 - 5.95: 29 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 119.70 125.64 -5.94 1.20e+00 6.94e-01 2.45e+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=" C3' A C 30 " pdb=" O3' A C 30 " pdb=" P A C 31 " ideal model delta sigma weight residual 119.70 123.48 -3.78 1.20e+00 6.94e-01 9.90e+00 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 ... (remaining 12709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 4720 35.70 - 71.39: 291 71.39 - 107.09: 12 107.09 - 142.78: 1 142.78 - 178.48: 3 Dihedral angle restraints: 5027 sinusoidal: 3163 harmonic: 1864 Sorted by residual: dihedral pdb=" C4' G C 2 " pdb=" C3' G C 2 " pdb=" C2' G C 2 " pdb=" C1' G C 2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.11 73.46 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' G C 56 " pdb=" C3' G C 56 " pdb=" C2' G C 56 " pdb=" C1' G C 56 " ideal model delta sinusoidal sigma weight residual 36.34 -36.59 72.93 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' U C 106 " pdb=" C3' U C 106 " pdb=" C2' U C 106 " pdb=" C1' U C 106 " ideal model delta sinusoidal sigma weight residual 36.34 -36.52 72.87 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 5024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1244 0.066 - 0.132: 67 0.132 - 0.199: 3 0.199 - 0.265: 161 0.265 - 0.331: 23 Chirality restraints: 1498 Sorted by residual: chirality pdb=" P A C 114 " pdb=" OP1 A C 114 " pdb=" OP2 A C 114 " pdb=" O5' A C 114 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" P U C 106 " pdb=" OP1 U C 106 " pdb=" OP2 U C 106 " pdb=" O5' U C 106 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" P A C 30 " pdb=" OP1 A C 30 " pdb=" OP2 A C 30 " pdb=" O5' A C 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (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: 0.530 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8862 Z= 0.146 Angle : 0.754 7.443 12714 Z= 0.387 Chirality : 0.090 0.331 1498 Planarity : 0.004 0.041 1088 Dihedral : 18.223 178.481 3809 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 638 TYR 0.033 0.002 TYR A 427 PHE 0.010 0.001 PHE A 398 TRP 0.010 0.001 TRP A 82 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 ( 8861) covalent geometry : angle 0.75371 / 0.39 (12714) hydrogen bonds : bond 0.29104 / 19.19 ( 294) hydrogen bonds : angle 10.14900 / 7.39 ( 767) metal coordination : bond 0.00034 / 0.02 ( 1) *********************** 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 : 0.248 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8049 (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: 0.1331 time to fit residues: 5.5790 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 : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3502 r_free = 0.3502 target = 0.049429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.040004 restraints weight = 133373.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.040755 restraints weight = 107065.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.041274 restraints weight = 90739.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.041680 restraints weight = 80357.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.041949 restraints weight = 73314.046| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8862 Z= 0.281 Angle : 1.223 13.669 12714 Z= 0.500 Chirality : 0.086 1.089 1498 Planarity : 0.006 0.052 1088 Dihedral : 18.023 176.684 2551 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.20 % Allowed : 3.62 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.32), residues: 628 helix: -0.02 (0.29), residues: 280 sheet: -2.94 (0.86), residues: 30 loop : -1.97 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 675 TYR 0.015 0.002 TYR A 427 PHE 0.019 0.002 PHE A 756 TRP 0.020 0.002 TRP A 724 HIS 0.002 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.28 ( 8861) covalent geometry : angle 1.22349 / 0.50 (12714) hydrogen bonds : bond 0.09531 / 6.32 ( 294) hydrogen bonds : angle 5.50762 / 4.05 ( 767) metal coordination : bond 0.00262 / 0.17 ( 1) *********************** 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 : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8376 (t-100) cc_final: 0.7895 (t-100) REVERT: A 371 ARG cc_start: 0.9232 (tpm170) cc_final: 0.8814 (tpm170) REVERT: A 377 TYR cc_start: 0.3240 (m-10) cc_final: 0.2777 (m-10) REVERT: A 450 ILE cc_start: 0.8878 (pt) cc_final: 0.8519 (mp) REVERT: A 580 MET cc_start: 0.7298 (mtt) cc_final: 0.6845 (mtt) REVERT: A 631 ASP cc_start: 0.9070 (m-30) cc_final: 0.8594 (p0) REVERT: A 683 ARG cc_start: 0.9622 (mmp80) cc_final: 0.9328 (mmp80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1381 time to fit residues: 5.7438 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 54 ASN A 115 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.047053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037864 restraints weight = 133019.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.038576 restraints weight = 106115.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.039090 restraints weight = 90120.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.039499 restraints weight = 79731.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.039677 restraints weight = 72448.002| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8862 Z= 0.221 Angle : 1.036 11.380 12714 Z= 0.432 Chirality : 0.071 0.443 1498 Planarity : 0.005 0.040 1088 Dihedral : 18.743 179.646 2551 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.32), residues: 628 helix: -0.08 (0.30), residues: 286 sheet: -2.90 (0.85), residues: 29 loop : -2.15 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 674 TYR 0.016 0.002 TYR A 175 PHE 0.017 0.003 PHE A 102 TRP 0.017 0.002 TRP A 724 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 ( 8861) covalent geometry : angle 1.03590 / 0.43 (12714) hydrogen bonds : bond 0.08195 / 5.45 ( 294) hydrogen bonds : angle 5.29209 / 3.86 ( 767) metal coordination : bond 0.00274 / 0.18 ( 1) *********************** 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 27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8309 (t-100) cc_final: 0.8022 (t-100) REVERT: A 377 TYR cc_start: 0.3631 (m-10) cc_final: 0.3294 (m-80) REVERT: A 631 ASP cc_start: 0.9018 (m-30) cc_final: 0.8437 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1625 time to fit residues: 5.6485 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.0270 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** 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 = 0.3431 r_free = 0.3431 target = 0.046474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.037260 restraints weight = 133902.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037984 restraints weight = 106321.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.038511 restraints weight = 89901.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.038880 restraints weight = 79487.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.039218 restraints weight = 72588.218| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8862 Z= 0.207 Angle : 1.013 11.578 12714 Z= 0.422 Chirality : 0.069 0.469 1498 Planarity : 0.006 0.070 1088 Dihedral : 18.649 174.331 2551 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.32), residues: 628 helix: 0.23 (0.30), residues: 275 sheet: -2.85 (0.87), residues: 29 loop : -2.32 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 508 TYR 0.016 0.002 TYR A 427 PHE 0.018 0.002 PHE A 756 TRP 0.019 0.002 TRP A 82 HIS 0.006 0.002 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 ( 8861) covalent geometry : angle 1.01265 / 0.42 (12714) hydrogen bonds : bond 0.07958 / 5.25 ( 294) hydrogen bonds : angle 5.30756 / 3.85 ( 767) metal coordination : bond 0.00073 / 0.05 ( 1) *********************** 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 24 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8287 (t-100) cc_final: 0.7971 (t-100) REVERT: A 377 TYR cc_start: 0.3134 (m-10) cc_final: 0.2867 (m-10) REVERT: A 628 MET cc_start: -0.1483 (ttt) cc_final: -0.4329 (ttt) REVERT: A 631 ASP cc_start: 0.9026 (m-30) cc_final: 0.8411 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1313 time to fit residues: 4.3165 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 : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 0.2980 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 62 GLN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.047966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.038491 restraints weight = 132917.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.039265 restraints weight = 105204.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.039792 restraints weight = 88225.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040222 restraints weight = 77753.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.040521 restraints weight = 70515.820| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8862 Z= 0.159 Angle : 0.938 11.318 12714 Z= 0.389 Chirality : 0.067 0.485 1498 Planarity : 0.005 0.062 1088 Dihedral : 18.553 174.286 2551 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.33), residues: 628 helix: 0.46 (0.31), residues: 271 sheet: -2.83 (0.87), residues: 29 loop : -2.25 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 619 TYR 0.015 0.001 TYR A 175 PHE 0.013 0.002 PHE A 81 TRP 0.022 0.002 TRP A 82 HIS 0.004 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 8861) covalent geometry : angle 0.93807 / 0.39 (12714) hydrogen bonds : bond 0.06525 / 4.37 ( 294) hydrogen bonds : angle 5.04376 / 3.65 ( 767) metal coordination : bond 0.00030 / 0.02 ( 1) *********************** 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 29 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.241 Fit side-chains REVERT: A 170 TRP cc_start: 0.8110 (t-100) cc_final: 0.7866 (t-100) REVERT: A 177 ARG cc_start: 0.8920 (mpt180) cc_final: 0.8437 (mmt180) REVERT: A 377 TYR cc_start: 0.3435 (m-10) cc_final: 0.3137 (m-10) REVERT: A 628 MET cc_start: -0.1883 (ttt) cc_final: -0.4852 (ttt) REVERT: A 631 ASP cc_start: 0.8833 (m-30) cc_final: 0.8120 (p0) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1499 time to fit residues: 5.6002 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 9 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** 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 = 0.3376 r_free = 0.3376 target = 0.043632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.034149 restraints weight = 138489.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034829 restraints weight = 110372.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.035415 restraints weight = 94022.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.035777 restraints weight = 82517.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.036134 restraints weight = 75176.490| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8862 Z= 0.298 Angle : 1.138 12.906 12714 Z= 0.477 Chirality : 0.073 0.518 1498 Planarity : 0.007 0.091 1088 Dihedral : 18.749 174.272 2551 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 39.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.32), residues: 628 helix: 0.01 (0.30), residues: 276 sheet: -3.28 (0.83), residues: 30 loop : -2.47 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 619 TYR 0.017 0.002 TYR A 393 PHE 0.025 0.003 PHE A 733 TRP 0.023 0.003 TRP A 82 HIS 0.007 0.002 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.30 ( 8861) covalent geometry : angle 1.13844 / 0.48 (12714) hydrogen bonds : bond 0.10420 / 6.71 ( 294) hydrogen bonds : angle 5.63233 / 4.08 ( 767) metal coordination : bond 0.00051 / 0.03 ( 1) *********************** 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 23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.242 Fit side-chains REVERT: A 170 TRP cc_start: 0.8527 (t-100) cc_final: 0.8106 (t-100) REVERT: A 177 ARG cc_start: 0.8527 (mpt180) cc_final: 0.8272 (mmt180) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1294 time to fit residues: 4.0995 Evaluate side-chains 16 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 681 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 = 0.3434 r_free = 0.3434 target = 0.045826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035940 restraints weight = 134114.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.036762 restraints weight = 106185.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.037314 restraints weight = 88990.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.037780 restraints weight = 78480.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.038084 restraints weight = 70666.302| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8862 Z= 0.188 Angle : 0.992 11.601 12714 Z= 0.413 Chirality : 0.069 0.485 1498 Planarity : 0.005 0.045 1088 Dihedral : 18.891 170.832 2551 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.33), residues: 628 helix: 0.23 (0.31), residues: 264 sheet: -2.91 (0.68), residues: 44 loop : -2.22 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 683 TYR 0.014 0.002 TYR A 175 PHE 0.014 0.002 PHE A 533 TRP 0.023 0.002 TRP A 82 HIS 0.005 0.002 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 8861) covalent geometry : angle 0.99169 / 0.41 (12714) hydrogen bonds : bond 0.07530 / 5.02 ( 294) hydrogen bonds : angle 5.33306 / 3.86 ( 767) metal coordination : bond 0.00039 / 0.03 ( 1) *********************** 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 23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8111 (t-100) cc_final: 0.7819 (t-100) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1126 time to fit residues: 3.7160 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 62 GLN A 146 GLN ** A 159 HIS ** 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 = 0.3529 r_free = 0.3529 target = 0.049224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.039199 restraints weight = 130966.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040028 restraints weight = 103330.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.040675 restraints weight = 86663.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.041144 restraints weight = 75579.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.041465 restraints weight = 68188.757| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8862 Z= 0.140 Angle : 0.918 10.882 12714 Z= 0.386 Chirality : 0.066 0.502 1498 Planarity : 0.005 0.074 1088 Dihedral : 18.517 170.352 2551 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.33), residues: 628 helix: 0.22 (0.31), residues: 269 sheet: -3.20 (0.84), residues: 30 loop : -2.23 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.012 0.001 TYR A 175 PHE 0.014 0.002 PHE A 533 TRP 0.025 0.002 TRP A 82 HIS 0.005 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8861) covalent geometry : angle 0.91781 / 0.39 (12714) hydrogen bonds : bond 0.05718 / 3.89 ( 294) hydrogen bonds : angle 4.91889 / 3.55 ( 767) metal coordination : bond 0.00022 / 0.01 ( 1) *********************** 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 to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.7965 (t-100) cc_final: 0.7705 (t-100) REVERT: A 177 ARG cc_start: 0.8798 (mpt180) cc_final: 0.8424 (mmt180) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1219 time to fit residues: 4.4072 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 : 0.233 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 47 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 32 optimal weight: 5.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 54 ASN ** A 146 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 = 0.3454 r_free = 0.3454 target = 0.046614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.036877 restraints weight = 132470.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.037640 restraints weight = 104622.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.038197 restraints weight = 87744.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.038640 restraints weight = 77364.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.038992 restraints weight = 69894.809| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8862 Z= 0.189 Angle : 0.951 10.836 12714 Z= 0.399 Chirality : 0.065 0.444 1498 Planarity : 0.005 0.041 1088 Dihedral : 18.556 173.651 2551 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.32), residues: 628 helix: 0.29 (0.31), residues: 267 sheet: -3.27 (0.81), residues: 30 loop : -2.25 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 619 TYR 0.012 0.002 TYR A 175 PHE 0.012 0.002 PHE A 533 TRP 0.021 0.002 TRP A 82 HIS 0.006 0.002 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 8861) covalent geometry : angle 0.95050 / 0.40 (12714) hydrogen bonds : bond 0.07111 / 4.75 ( 294) hydrogen bonds : angle 5.14324 / 3.74 ( 767) metal coordination : bond 0.00020 / 0.01 ( 1) *********************** 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 24 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.7981 (t-100) cc_final: 0.7669 (t-100) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1218 time to fit residues: 4.0519 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 53 optimal weight: 0.0970 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.044990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.035425 restraints weight = 135173.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036245 restraints weight = 106594.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.036775 restraints weight = 89290.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.037231 restraints weight = 78661.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.037509 restraints weight = 70944.878| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8862 Z= 0.223 Angle : 1.013 10.361 12714 Z= 0.430 Chirality : 0.067 0.435 1498 Planarity : 0.006 0.111 1088 Dihedral : 18.716 172.638 2551 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 33.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.32), residues: 628 helix: 0.05 (0.31), residues: 267 sheet: -3.10 (0.62), residues: 44 loop : -2.27 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 619 TYR 0.014 0.002 TYR A 175 PHE 0.018 0.003 PHE A 85 TRP 0.020 0.002 TRP A 82 HIS 0.004 0.002 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 ( 8861) covalent geometry : angle 1.01316 / 0.43 (12714) hydrogen bonds : bond 0.07895 / 5.22 ( 294) hydrogen bonds : angle 5.30522 / 3.87 ( 767) metal coordination : bond 0.00045 / 0.03 ( 1) ********************** 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 23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8005 (t-100) cc_final: 0.7681 (t-100) REVERT: A 177 ARG cc_start: 0.8718 (mpt180) cc_final: 0.8391 (mmt180) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1054 time to fit residues: 3.6831 Evaluate side-chains 18 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.034732 restraints weight = 135855.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035548 restraints weight = 106947.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.036077 restraints weight = 89424.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036527 restraints weight = 78830.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.036828 restraints weight = 70840.440| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8862 Z= 0.232 Angle : 1.030 10.407 12714 Z= 0.436 Chirality : 0.068 0.417 1498 Planarity : 0.006 0.073 1088 Dihedral : 18.853 170.239 2551 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 34.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.32), residues: 628 helix: -0.05 (0.31), residues: 262 sheet: -3.16 (0.62), residues: 44 loop : -2.25 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 575 TYR 0.014 0.002 TYR A 393 PHE 0.015 0.002 PHE A 533 TRP 0.025 0.002 TRP A 82 HIS 0.005 0.002 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 ( 8861) covalent geometry : angle 1.03024 / 0.44 (12714) hydrogen bonds : bond 0.08251 / 5.46 ( 294) hydrogen bonds : angle 5.36266 / 3.92 ( 767) metal coordination : bond 0.00025 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1379.60 seconds wall clock time: 24 minutes 46.73 seconds (1486.73 seconds total)