Starting phenix.real_space_refine on Sat May 17 21:52:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056.map" model { file = "/net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q0n_18056/05_2025/8q0n_18056_trim.cif" } resolution = 4.2 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= 0.009 sd= 0.124 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 P 3 5.49 5 S 56 5.16 5 C 5080 2.51 5 N 1360 2.21 5 O 1508 1.98 5 H 7910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15917 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 13084 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 39, 'TRANS': 791} Chain breaks: 2 Chain: "C" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2798 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'04E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'04E:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.47, per 1000 atoms: 0.47 Number of scatterers: 15917 At special positions: 0 Unit cell: (80.898, 92.574, 146.784, 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) S 56 16.00 P 3 15.00 O 1508 8.00 N 1360 7.00 C 5080 6.00 H 7910 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 65.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 26 through 41 Proline residue: B 36 - end of helix removed outlier: 4.193A pdb=" N MET B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.594A pdb=" N SER B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.776A pdb=" N LEU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.578A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.875A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.965A pdb=" N VAL B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.032A pdb=" N LEU B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.511A pdb=" N CYS B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.265A pdb=" N GLN B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.720A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 312 through 333 removed outlier: 3.556A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.587A pdb=" N VAL B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 395 removed outlier: 3.655A pdb=" N LEU B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 465 removed outlier: 3.542A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 3.616A pdb=" N PHE B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 495 through 501 removed outlier: 4.323A pdb=" N PHE B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.650A pdb=" N LEU B 506 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.875A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 522 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 538 removed outlier: 3.720A pdb=" N TRP B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 534 " --> pdb=" O TRP B 530 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 574 through 580 Processing helix chain 'B' and resid 593 through 610 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.537A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 655 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 676 through 683 Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 736 through 750 removed outlier: 3.843A pdb=" N GLU B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 765 Processing helix chain 'B' and resid 769 through 775 removed outlier: 3.668A pdb=" N LEU B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 787 Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'B' and resid 809 through 823 Processing helix chain 'B' and resid 824 through 837 removed outlier: 3.525A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.873A pdb=" N ALA B 847 " --> pdb=" O GLY B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.790A pdb=" N ARG C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.511A pdb=" N PHE C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.790A pdb=" N ILE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.607A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 178 removed outlier: 3.767A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.664A pdb=" N PHE B 61 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 66 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 555 through 557 removed outlier: 5.298A pdb=" N LEU B 555 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 616 through 618 Processing sheet with id=AA4, first strand: chain 'B' and resid 709 through 714 removed outlier: 3.596A pdb=" N VAL B 710 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 721 " --> pdb=" O VAL B 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 850 through 851 removed outlier: 3.529A pdb=" N GLY B 854 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 859 through 863 Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 46 removed outlier: 4.044A pdb=" N ASP C 38 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 57 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 2 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL C 77 " --> pdb=" O ALA C 3 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N SER C 83 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 153 " --> pdb=" O ILE C 110 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7882 1.03 - 1.23: 119 1.23 - 1.43: 3302 1.43 - 1.62: 4706 1.62 - 1.82: 83 Bond restraints: 16092 Sorted by residual: bond pdb=" N GLU B 22 " pdb=" CA GLU B 22 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 22 " pdb=" H GLU B 22 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N MET C 1 " pdb=" H MET C 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 04E B1001 " pdb=" O1 04E B1001 " ideal model delta sigma weight residual 1.235 1.259 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 16087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 28447 1.41 - 2.81: 599 2.81 - 4.22: 43 4.22 - 5.63: 11 5.63 - 7.03: 1 Bond angle restraints: 29101 Sorted by residual: angle pdb=" C2' GTP C 201 " pdb=" C3' GTP C 201 " pdb=" C4' GTP C 201 " ideal model delta sigma weight residual 111.00 103.97 7.03 3.00e+00 1.11e-01 5.50e+00 angle pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " pdb=" CG GLN B 774 " ideal model delta sigma weight residual 114.10 118.70 -4.60 2.00e+00 2.50e-01 5.29e+00 angle pdb=" CA MET B 37 " pdb=" CB MET B 37 " pdb=" CG MET B 37 " ideal model delta sigma weight residual 114.10 118.56 -4.46 2.00e+00 2.50e-01 4.96e+00 angle pdb=" N TYR C 72 " pdb=" CA TYR C 72 " pdb=" C TYR C 72 " ideal model delta sigma weight residual 109.81 114.45 -4.64 2.21e+00 2.05e-01 4.41e+00 angle pdb=" C ARG B 655 " pdb=" CA ARG B 655 " pdb=" CB ARG B 655 " ideal model delta sigma weight residual 111.06 107.66 3.40 1.83e+00 2.99e-01 3.45e+00 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 7355 29.79 - 59.59: 227 59.59 - 89.38: 13 89.38 - 119.18: 0 119.18 - 148.97: 2 Dihedral angle restraints: 7597 sinusoidal: 4152 harmonic: 3445 Sorted by residual: dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 -141.76 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -23.95 128.54 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CG LYS B 488 " pdb=" CD LYS B 488 " pdb=" CE LYS B 488 " pdb=" NZ LYS B 488 " ideal model delta sinusoidal sigma weight residual 180.00 121.70 58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 838 0.027 - 0.054: 261 0.054 - 0.081: 92 0.081 - 0.108: 43 0.108 - 0.135: 23 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO B 200 " pdb=" N PRO B 200 " pdb=" C PRO B 200 " pdb=" CB PRO B 200 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE B 860 " pdb=" N ILE B 860 " pdb=" C ILE B 860 " pdb=" CB ILE B 860 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1254 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 68 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 69 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 788 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 789 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 789 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 789 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 33 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 34 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.020 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 943 2.20 - 2.80: 32970 2.80 - 3.40: 43521 3.40 - 4.00: 54471 4.00 - 4.60: 83996 Nonbonded interactions: 215901 Sorted by model distance: nonbonded pdb=" OE1 GLU B 285 " pdb=" H GLU B 285 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP C 11 " pdb=" HE1 TRP C 97 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASP C 65 " pdb="HH22 ARG C 68 " model vdw 1.667 2.450 nonbonded pdb=" OE1 GLN B 756 " pdb=" H GLN B 756 " model vdw 1.677 2.450 nonbonded pdb=" H THR B 733 " pdb=" OD1 ASN B 736 " model vdw 1.680 2.450 ... (remaining 215896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.260 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4431 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 0.199 8184 Z= 0.240 Angle : 0.477 7.034 11113 Z= 0.239 Chirality : 0.036 0.135 1257 Planarity : 0.004 0.055 1431 Dihedral : 13.782 148.971 3024 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.28 (0.27), residues: 1001 helix: 1.36 (0.22), residues: 544 sheet: 0.59 (0.76), residues: 50 loop : 0.34 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.007 0.001 HIS B 637 PHE 0.015 0.001 PHE C 37 TYR 0.013 0.001 TYR B 313 ARG 0.007 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.25984 ( 419) hydrogen bonds : angle 7.62510 ( 1221) covalent geometry : bond 0.00206 ( 8182) covalent geometry : angle 0.47664 (11113) Misc. bond : bond 0.14136 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.4626 (p90) cc_final: 0.4300 (p90) REVERT: B 114 MET cc_start: 0.3889 (mmt) cc_final: 0.3679 (mmt) REVERT: B 312 ASN cc_start: 0.9012 (t0) cc_final: 0.8805 (t0) REVERT: B 634 ASN cc_start: 0.7705 (t0) cc_final: 0.7495 (t0) REVERT: B 718 MET cc_start: 0.5410 (tpp) cc_final: 0.5079 (tpp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3968 time to fit residues: 80.9062 Evaluate side-chains 128 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 173 GLN B 302 ASN B 697 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.183790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.153351 restraints weight = 36243.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.158226 restraints weight = 35627.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160336 restraints weight = 16583.502| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8184 Z= 0.184 Angle : 0.598 7.727 11113 Z= 0.321 Chirality : 0.040 0.145 1257 Planarity : 0.005 0.056 1431 Dihedral : 7.953 166.154 1094 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1001 helix: 0.97 (0.21), residues: 586 sheet: 0.12 (0.73), residues: 50 loop : 0.35 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 97 HIS 0.007 0.002 HIS B 252 PHE 0.009 0.002 PHE B 203 TYR 0.014 0.002 TYR B 202 ARG 0.004 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 419) hydrogen bonds : angle 5.68038 ( 1221) covalent geometry : bond 0.00394 ( 8182) covalent geometry : angle 0.59800 (11113) Misc. bond : bond 0.00091 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 MET cc_start: 0.7386 (mmt) cc_final: 0.6871 (mmt) REVERT: B 209 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8006 (mm-40) REVERT: B 243 GLU cc_start: 0.5560 (tp30) cc_final: 0.5346 (tp30) REVERT: B 530 TRP cc_start: 0.7299 (t60) cc_final: 0.6843 (t60) REVERT: B 646 GLN cc_start: 0.6876 (mt0) cc_final: 0.6208 (mt0) REVERT: B 718 MET cc_start: 0.5214 (tpp) cc_final: 0.4713 (tpp) REVERT: B 742 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 743 LEU cc_start: 0.8930 (mm) cc_final: 0.8502 (mm) REVERT: B 846 PHE cc_start: 0.6312 (m-80) cc_final: 0.6063 (m-80) REVERT: C 75 THR cc_start: 0.7468 (m) cc_final: 0.7014 (m) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4405 time to fit residues: 87.6469 Evaluate side-chains 116 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 656 GLN ** C 141 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 = 0.4422 r_free = 0.4422 target = 0.181754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147894 restraints weight = 36442.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154450 restraints weight = 36674.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.155374 restraints weight = 18509.072| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8184 Z= 0.123 Angle : 0.508 6.864 11113 Z= 0.268 Chirality : 0.038 0.137 1257 Planarity : 0.004 0.056 1431 Dihedral : 8.007 176.949 1094 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 1.00 (0.27), residues: 1001 helix: 1.03 (0.21), residues: 587 sheet: 0.22 (0.74), residues: 48 loop : 0.33 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 97 HIS 0.005 0.001 HIS B 637 PHE 0.013 0.001 PHE B 459 TYR 0.011 0.001 TYR B 313 ARG 0.003 0.000 ARG B 475 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 419) hydrogen bonds : angle 5.22732 ( 1221) covalent geometry : bond 0.00258 ( 8182) covalent geometry : angle 0.50827 (11113) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8033 (t0) cc_final: 0.7587 (p0) REVERT: B 92 ASN cc_start: 0.7878 (t0) cc_final: 0.7650 (t0) REVERT: B 114 MET cc_start: 0.7307 (mmt) cc_final: 0.6950 (mmt) REVERT: B 209 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 530 TRP cc_start: 0.7292 (t60) cc_final: 0.6901 (t60) REVERT: B 646 GLN cc_start: 0.6686 (mt0) cc_final: 0.6197 (mt0) REVERT: B 718 MET cc_start: 0.5198 (tpp) cc_final: 0.4711 (tpp) REVERT: B 846 PHE cc_start: 0.6350 (m-80) cc_final: 0.6069 (m-80) REVERT: C 75 THR cc_start: 0.7360 (m) cc_final: 0.6812 (m) REVERT: C 119 LEU cc_start: 0.7623 (mm) cc_final: 0.7390 (mm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3805 time to fit residues: 73.6331 Evaluate side-chains 113 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 594 GLN C 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.178245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.142543 restraints weight = 37430.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.142953 restraints weight = 24625.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.144859 restraints weight = 20457.584| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8184 Z= 0.115 Angle : 0.502 7.086 11113 Z= 0.263 Chirality : 0.037 0.137 1257 Planarity : 0.005 0.101 1431 Dihedral : 7.975 177.653 1094 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 0.78 % Favored : 99.11 % 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: 0.95 (0.27), residues: 1001 helix: 0.96 (0.21), residues: 588 sheet: 0.35 (0.77), residues: 48 loop : 0.34 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 364 HIS 0.004 0.001 HIS B 637 PHE 0.013 0.001 PHE B 327 TYR 0.009 0.001 TYR B 202 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 419) hydrogen bonds : angle 5.11209 ( 1221) covalent geometry : bond 0.00248 ( 8182) covalent geometry : angle 0.50210 (11113) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8208 (t0) cc_final: 0.7707 (p0) REVERT: B 114 MET cc_start: 0.7019 (mmt) cc_final: 0.6807 (mmt) REVERT: B 209 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7893 (mm-40) REVERT: B 278 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6998 (mt-10) REVERT: B 530 TRP cc_start: 0.7229 (t60) cc_final: 0.6870 (t60) REVERT: B 646 GLN cc_start: 0.7050 (mt0) cc_final: 0.6450 (mt0) REVERT: B 718 MET cc_start: 0.5423 (tpp) cc_final: 0.4864 (tpp) REVERT: B 742 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 743 LEU cc_start: 0.9206 (mm) cc_final: 0.8906 (mm) REVERT: C 75 THR cc_start: 0.7361 (m) cc_final: 0.6793 (m) REVERT: C 119 LEU cc_start: 0.7670 (mm) cc_final: 0.7382 (mt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.3503 time to fit residues: 68.6261 Evaluate side-chains 114 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.0050 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.177418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.144120 restraints weight = 37433.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143642 restraints weight = 33128.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146909 restraints weight = 23624.962| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8184 Z= 0.164 Angle : 0.557 7.320 11113 Z= 0.297 Chirality : 0.039 0.164 1257 Planarity : 0.005 0.067 1431 Dihedral : 8.280 177.577 1094 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 0.63 (0.27), residues: 1001 helix: 0.73 (0.21), residues: 589 sheet: -0.38 (0.76), residues: 48 loop : 0.25 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 364 HIS 0.011 0.001 HIS B 148 PHE 0.015 0.002 PHE B 479 TYR 0.013 0.002 TYR B 288 ARG 0.004 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 419) hydrogen bonds : angle 5.22619 ( 1221) covalent geometry : bond 0.00357 ( 8182) covalent geometry : angle 0.55728 (11113) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8286 (t0) cc_final: 0.7780 (p0) REVERT: B 92 ASN cc_start: 0.7959 (t0) cc_final: 0.7757 (t0) REVERT: B 159 VAL cc_start: 0.8825 (m) cc_final: 0.8602 (p) REVERT: B 163 MET cc_start: 0.5308 (ptm) cc_final: 0.4735 (ptm) REVERT: B 184 LEU cc_start: 0.7332 (mm) cc_final: 0.7116 (mm) REVERT: B 209 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7977 (mm-40) REVERT: B 646 GLN cc_start: 0.6680 (mt0) cc_final: 0.6191 (mt0) REVERT: B 718 MET cc_start: 0.5330 (tpp) cc_final: 0.4777 (tpp) REVERT: B 767 PHE cc_start: 0.8269 (m-80) cc_final: 0.7914 (m-10) REVERT: C 75 THR cc_start: 0.7462 (m) cc_final: 0.6908 (m) REVERT: C 119 LEU cc_start: 0.7672 (mm) cc_final: 0.7388 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4243 time to fit residues: 80.4177 Evaluate side-chains 107 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.179814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146582 restraints weight = 36581.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149059 restraints weight = 33143.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151251 restraints weight = 21207.484| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8184 Z= 0.106 Angle : 0.499 6.666 11113 Z= 0.260 Chirality : 0.037 0.138 1257 Planarity : 0.004 0.047 1431 Dihedral : 7.953 171.891 1094 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 1.00 (0.27), residues: 1001 helix: 1.06 (0.21), residues: 587 sheet: -0.20 (0.77), residues: 47 loop : 0.35 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 364 HIS 0.004 0.001 HIS B 503 PHE 0.015 0.001 PHE B 502 TYR 0.016 0.001 TYR B 241 ARG 0.002 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 419) hydrogen bonds : angle 4.94293 ( 1221) covalent geometry : bond 0.00230 ( 8182) covalent geometry : angle 0.49922 (11113) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8237 (t0) cc_final: 0.7680 (p0) REVERT: B 92 ASN cc_start: 0.7921 (t0) cc_final: 0.7685 (t0) REVERT: B 114 MET cc_start: 0.7231 (mmt) cc_final: 0.6447 (mmt) REVERT: B 159 VAL cc_start: 0.8783 (m) cc_final: 0.8555 (p) REVERT: B 163 MET cc_start: 0.5287 (ptm) cc_final: 0.4895 (ptm) REVERT: B 184 LEU cc_start: 0.7367 (mm) cc_final: 0.7161 (mm) REVERT: B 209 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7745 (mm-40) REVERT: B 278 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 646 GLN cc_start: 0.6662 (mt0) cc_final: 0.6141 (mt0) REVERT: B 718 MET cc_start: 0.5323 (tpp) cc_final: 0.4776 (tpp) REVERT: B 767 PHE cc_start: 0.8221 (m-80) cc_final: 0.7915 (m-10) REVERT: C 75 THR cc_start: 0.7277 (m) cc_final: 0.6726 (m) REVERT: C 119 LEU cc_start: 0.7638 (mm) cc_final: 0.7403 (mt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3833 time to fit residues: 72.0412 Evaluate side-chains 109 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.178072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145519 restraints weight = 36944.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.144603 restraints weight = 29678.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147016 restraints weight = 26046.661| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8184 Z= 0.133 Angle : 0.518 7.079 11113 Z= 0.273 Chirality : 0.038 0.143 1257 Planarity : 0.004 0.049 1431 Dihedral : 7.978 170.185 1094 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.82 (0.27), residues: 1001 helix: 0.97 (0.21), residues: 584 sheet: -0.78 (0.75), residues: 48 loop : 0.24 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.010 0.001 HIS B 207 PHE 0.016 0.001 PHE B 479 TYR 0.010 0.001 TYR B 288 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 419) hydrogen bonds : angle 5.00244 ( 1221) covalent geometry : bond 0.00292 ( 8182) covalent geometry : angle 0.51823 (11113) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8352 (t0) cc_final: 0.7701 (p0) REVERT: B 92 ASN cc_start: 0.7992 (t0) cc_final: 0.7713 (t0) REVERT: B 159 VAL cc_start: 0.8761 (m) cc_final: 0.8537 (p) REVERT: B 163 MET cc_start: 0.5705 (ptm) cc_final: 0.5343 (ptm) REVERT: B 184 LEU cc_start: 0.7354 (mm) cc_final: 0.7114 (mm) REVERT: B 209 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7820 (mm-40) REVERT: B 646 GLN cc_start: 0.6771 (mt0) cc_final: 0.6293 (mt0) REVERT: B 718 MET cc_start: 0.5361 (tpp) cc_final: 0.4791 (tpp) REVERT: B 767 PHE cc_start: 0.8270 (m-80) cc_final: 0.7904 (m-10) REVERT: C 75 THR cc_start: 0.7348 (m) cc_final: 0.6786 (m) REVERT: C 119 LEU cc_start: 0.7674 (mm) cc_final: 0.7419 (mt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4161 time to fit residues: 75.7264 Evaluate side-chains 111 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 28 optimal weight: 0.0870 chunk 96 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.179686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145489 restraints weight = 36671.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146649 restraints weight = 35924.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.149746 restraints weight = 24119.391| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8184 Z= 0.104 Angle : 0.490 6.587 11113 Z= 0.254 Chirality : 0.037 0.136 1257 Planarity : 0.004 0.047 1431 Dihedral : 7.796 166.984 1094 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.98 (0.27), residues: 1001 helix: 1.14 (0.21), residues: 589 sheet: -0.81 (0.76), residues: 49 loop : 0.25 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 364 HIS 0.006 0.001 HIS B 207 PHE 0.014 0.001 PHE B 479 TYR 0.008 0.001 TYR B 313 ARG 0.002 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 419) hydrogen bonds : angle 4.82503 ( 1221) covalent geometry : bond 0.00227 ( 8182) covalent geometry : angle 0.49014 (11113) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8334 (t0) cc_final: 0.7706 (p0) REVERT: B 92 ASN cc_start: 0.7970 (t0) cc_final: 0.7711 (t0) REVERT: B 114 MET cc_start: 0.7203 (mmt) cc_final: 0.6660 (mmt) REVERT: B 159 VAL cc_start: 0.8776 (m) cc_final: 0.8539 (p) REVERT: B 163 MET cc_start: 0.5689 (ptm) cc_final: 0.5411 (ptm) REVERT: B 209 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7772 (mm-40) REVERT: B 467 MET cc_start: 0.4348 (ptt) cc_final: 0.4146 (ptt) REVERT: B 646 GLN cc_start: 0.6700 (mt0) cc_final: 0.6223 (mt0) REVERT: B 718 MET cc_start: 0.5404 (tpp) cc_final: 0.4835 (tpp) REVERT: B 767 PHE cc_start: 0.8239 (m-80) cc_final: 0.7848 (m-10) REVERT: C 75 THR cc_start: 0.7273 (m) cc_final: 0.6682 (m) REVERT: C 119 LEU cc_start: 0.7618 (mm) cc_final: 0.7351 (mt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4402 time to fit residues: 79.0189 Evaluate side-chains 112 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.179419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146939 restraints weight = 36814.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145828 restraints weight = 33064.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149353 restraints weight = 26285.098| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8184 Z= 0.130 Angle : 0.518 6.894 11113 Z= 0.271 Chirality : 0.038 0.140 1257 Planarity : 0.004 0.048 1431 Dihedral : 7.852 164.728 1094 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.86 (0.27), residues: 1001 helix: 1.04 (0.21), residues: 589 sheet: -1.14 (0.75), residues: 48 loop : 0.23 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 693 HIS 0.006 0.001 HIS B 207 PHE 0.010 0.001 PHE B 256 TYR 0.010 0.001 TYR B 202 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 419) hydrogen bonds : angle 4.90200 ( 1221) covalent geometry : bond 0.00286 ( 8182) covalent geometry : angle 0.51751 (11113) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8353 (t0) cc_final: 0.7752 (p0) REVERT: B 92 ASN cc_start: 0.7974 (t0) cc_final: 0.7692 (t0) REVERT: B 159 VAL cc_start: 0.8771 (m) cc_final: 0.8561 (p) REVERT: B 163 MET cc_start: 0.5923 (ptm) cc_final: 0.5650 (ptm) REVERT: B 209 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7861 (mm-40) REVERT: B 646 GLN cc_start: 0.6760 (mt0) cc_final: 0.6344 (mt0) REVERT: B 718 MET cc_start: 0.5419 (tpp) cc_final: 0.4827 (tpp) REVERT: B 767 PHE cc_start: 0.8290 (m-80) cc_final: 0.7958 (m-10) REVERT: C 75 THR cc_start: 0.7353 (m) cc_final: 0.6763 (m) REVERT: C 119 LEU cc_start: 0.7639 (mm) cc_final: 0.7367 (mt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4038 time to fit residues: 74.1167 Evaluate side-chains 110 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.176631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144556 restraints weight = 36604.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145202 restraints weight = 39480.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147806 restraints weight = 26992.153| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8184 Z= 0.177 Angle : 0.582 7.217 11113 Z= 0.312 Chirality : 0.040 0.150 1257 Planarity : 0.005 0.052 1431 Dihedral : 8.186 163.307 1094 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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: 0.38 (0.27), residues: 1001 helix: 0.74 (0.21), residues: 587 sheet: -1.87 (0.70), residues: 48 loop : -0.03 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 56 HIS 0.007 0.001 HIS B 279 PHE 0.015 0.002 PHE B 479 TYR 0.013 0.002 TYR B 202 ARG 0.004 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 419) hydrogen bonds : angle 5.20689 ( 1221) covalent geometry : bond 0.00389 ( 8182) covalent geometry : angle 0.58229 (11113) Misc. bond : bond 0.00011 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8519 (t0) cc_final: 0.7959 (p0) REVERT: B 92 ASN cc_start: 0.8044 (t0) cc_final: 0.7780 (t0) REVERT: B 159 VAL cc_start: 0.8759 (m) cc_final: 0.8539 (p) REVERT: B 209 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8042 (mm-40) REVERT: B 646 GLN cc_start: 0.6941 (mt0) cc_final: 0.6588 (mt0) REVERT: B 718 MET cc_start: 0.5490 (tpp) cc_final: 0.4879 (tpp) REVERT: B 767 PHE cc_start: 0.8362 (m-80) cc_final: 0.8085 (m-10) REVERT: B 848 ASN cc_start: 0.7492 (t0) cc_final: 0.7133 (t0) REVERT: C 119 LEU cc_start: 0.7729 (mm) cc_final: 0.7449 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4062 time to fit residues: 73.3461 Evaluate side-chains 111 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.177016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.143326 restraints weight = 36455.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.143357 restraints weight = 29622.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.145571 restraints weight = 23629.786| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8184 Z= 0.113 Angle : 0.508 6.581 11113 Z= 0.266 Chirality : 0.038 0.138 1257 Planarity : 0.004 0.053 1431 Dihedral : 7.722 155.577 1094 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 0.77 (0.27), residues: 1001 helix: 1.06 (0.21), residues: 581 sheet: -1.63 (0.74), residues: 47 loop : 0.12 (0.36), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 56 HIS 0.004 0.001 HIS B 503 PHE 0.013 0.001 PHE B 531 TYR 0.014 0.001 TYR B 288 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 419) hydrogen bonds : angle 4.91741 ( 1221) covalent geometry : bond 0.00249 ( 8182) covalent geometry : angle 0.50827 (11113) Misc. bond : bond 0.00003 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4733.04 seconds wall clock time: 82 minutes 41.80 seconds (4961.80 seconds total)