Starting phenix.real_space_refine on Sat Jun 14 13:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q0n_18056/06_2025/8q0n_18056_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q0n_18056/06_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_18056/06_2025/8q0n_18056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q0n_18056/06_2025/8q0n_18056.map" model { file = "/net/cci-nas-00/data/ceres_data/8q0n_18056/06_2025/8q0n_18056_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q0n_18056/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.63, per 1000 atoms: 0.48 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: 4.06 Conformation dependent library (CDL) restraints added in 1.1 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: 1.22 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: 5.66 Time building geometry restraints manager: 4.95 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- 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 : 1.110 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: 0.3911 time to fit residues: 80.0041 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 : 1.276 ------------------------------------------------------------------------------- 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 = 0.158228 restraints weight = 35628.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160336 restraints weight = 16581.235| |-----------------------------------------------------------------------------| 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 : 1.258 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: 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: 0.8007 (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: 0.6209 (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: 0.8024 (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: 0.3972 time to fit residues: 77.9227 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 : 1.220 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 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 = 0.181706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.147131 restraints weight = 36448.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.151643 restraints weight = 36748.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153459 restraints weight = 22189.522| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2071 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= 0.124 Angle : 0.508 6.856 11113 Z= 0.268 Chirality : 0.038 0.137 1257 Planarity : 0.004 0.056 1431 Dihedral : 8.009 177.058 1094 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.33 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: 1.01 (0.27), residues: 1001 helix: 1.04 (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 0.04950 ( 419) hydrogen bonds : angle 5.22378 ( 1221) covalent geometry : bond 0.00258 ( 8182) covalent geometry : angle 0.50823 (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 : 1.136 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: 0.8049 (t0) cc_final: 0.7592 (p0) REVERT: B 92 ASN cc_start: 0.7894 (t0) cc_final: 0.7660 (t0) REVERT: B 114 MET cc_start: 0.7303 (mmt) cc_final: 0.6943 (mmt) REVERT: B 209 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7822 (mm-40) REVERT: B 530 TRP cc_start: 0.7304 (t60) cc_final: 0.6911 (t60) REVERT: B 646 GLN cc_start: 0.6712 (mt0) cc_final: 0.6221 (mt0) REVERT: B 718 MET cc_start: 0.5263 (tpp) cc_final: 0.4753 (tpp) REVERT: B 846 PHE cc_start: 0.6401 (m-80) cc_final: 0.6077 (m-80) REVERT: C 75 THR cc_start: 0.7356 (m) cc_final: 0.6818 (m) REVERT: C 119 LEU cc_start: 0.7615 (mm) cc_final: 0.7381 (mm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3795 time to fit residues: 73.6600 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 : 1.135 ------------------------------------------------------------------------------- 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: 0.4980 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 GLN C 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.178747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.143250 restraints weight = 37523.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144919 restraints weight = 24854.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146533 restraints weight = 19667.531| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8184 Z= 0.112 Angle : 0.502 7.024 11113 Z= 0.263 Chirality : 0.037 0.137 1257 Planarity : 0.005 0.101 1431 Dihedral : 7.946 177.256 1094 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 0.67 % Favored : 99.22 % 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: 0.96 (0.27), residues: 1001 helix: 0.96 (0.21), residues: 590 sheet: 0.41 (0.77), residues: 48 loop : 0.34 (0.35), residues: 363 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 313 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 419) hydrogen bonds : angle 5.08546 ( 1221) covalent geometry : bond 0.00240 ( 8182) covalent geometry : angle 0.50160 (11113) Misc. bond : bond 0.00009 ( 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 137 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.199 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: 0.8192 (t0) cc_final: 0.7675 (p0) REVERT: B 114 MET cc_start: 0.7009 (mmt) cc_final: 0.6803 (mmt) REVERT: B 209 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7880 (mm-40) REVERT: B 278 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 530 TRP cc_start: 0.7190 (t60) cc_final: 0.6826 (t60) REVERT: B 646 GLN cc_start: 0.7029 (mt0) cc_final: 0.6434 (mt0) REVERT: B 718 MET cc_start: 0.5430 (tpp) cc_final: 0.4873 (tpp) REVERT: B 742 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 743 LEU cc_start: 0.9205 (mm) cc_final: 0.8906 (mm) REVERT: C 75 THR cc_start: 0.7327 (m) cc_final: 0.6766 (m) REVERT: C 119 LEU cc_start: 0.7671 (mm) cc_final: 0.7381 (mt) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.3620 time to fit residues: 71.8084 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 : 1.277 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.177216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.144047 restraints weight = 37288.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143275 restraints weight = 31403.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.145134 restraints weight = 26816.373| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2944 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= 0.169 Angle : 0.561 7.264 11113 Z= 0.300 Chirality : 0.039 0.170 1257 Planarity : 0.005 0.070 1431 Dihedral : 8.304 176.959 1094 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.91 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: 0.65 (0.27), residues: 1001 helix: 0.76 (0.21), residues: 592 sheet: -0.49 (0.75), residues: 48 loop : 0.24 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 364 HIS 0.009 0.001 HIS B 252 PHE 0.015 0.002 PHE B 479 TYR 0.014 0.002 TYR B 288 ARG 0.004 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 419) hydrogen bonds : angle 5.28161 ( 1221) covalent geometry : bond 0.00369 ( 8182) covalent geometry : angle 0.56145 (11113) Misc. bond : bond 0.00023 ( 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 : 1.229 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: 0.8314 (t0) cc_final: 0.7784 (p0) REVERT: B 92 ASN cc_start: 0.7977 (t0) cc_final: 0.7777 (t0) REVERT: B 184 LEU cc_start: 0.7336 (mm) cc_final: 0.7118 (mm) REVERT: B 209 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7960 (mm-40) REVERT: B 630 ASN cc_start: 0.8116 (t0) cc_final: 0.7848 (m110) REVERT: B 646 GLN cc_start: 0.6757 (mt0) cc_final: 0.6267 (mt0) REVERT: B 718 MET cc_start: 0.5369 (tpp) cc_final: 0.4803 (tpp) REVERT: B 767 PHE cc_start: 0.8305 (m-80) cc_final: 0.7896 (m-10) REVERT: C 75 THR cc_start: 0.7520 (m) cc_final: 0.6963 (m) REVERT: C 119 LEU cc_start: 0.7689 (mm) cc_final: 0.7438 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3637 time to fit residues: 68.4079 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 : 1.145 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.178813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.145607 restraints weight = 37010.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145192 restraints weight = 30404.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.147972 restraints weight = 24399.573| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8184 Z= 0.147 Angle : 0.533 6.666 11113 Z= 0.282 Chirality : 0.038 0.142 1257 Planarity : 0.005 0.049 1431 Dihedral : 8.095 167.416 1094 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.61 (0.27), residues: 1001 helix: 0.86 (0.21), residues: 585 sheet: -1.13 (0.75), residues: 48 loop : 0.10 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.006 0.001 HIS B 279 PHE 0.018 0.002 PHE B 502 TYR 0.022 0.002 TYR B 241 ARG 0.004 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 419) hydrogen bonds : angle 5.15111 ( 1221) covalent geometry : bond 0.00319 ( 8182) covalent geometry : angle 0.53298 (11113) Misc. bond : bond 0.00006 ( 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 130 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.208 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: 0.8328 (t0) cc_final: 0.7707 (p0) REVERT: B 92 ASN cc_start: 0.7953 (t0) cc_final: 0.7697 (t0) REVERT: B 114 MET cc_start: 0.7367 (mmt) cc_final: 0.6856 (mmt) REVERT: B 159 VAL cc_start: 0.8774 (m) cc_final: 0.8530 (p) REVERT: B 163 MET cc_start: 0.5710 (ptm) cc_final: 0.5372 (ptm) REVERT: B 209 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7877 (mm-40) REVERT: B 630 ASN cc_start: 0.8010 (t0) cc_final: 0.7797 (m110) REVERT: B 646 GLN cc_start: 0.6764 (mt0) cc_final: 0.6298 (mt0) REVERT: B 718 MET cc_start: 0.5359 (tpp) cc_final: 0.4810 (tpp) REVERT: B 767 PHE cc_start: 0.8285 (m-80) cc_final: 0.7950 (m-10) REVERT: C 75 THR cc_start: 0.7455 (m) cc_final: 0.6890 (m) REVERT: C 119 LEU cc_start: 0.7667 (mm) cc_final: 0.7441 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3959 time to fit residues: 72.3053 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 : 1.238 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.180676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146733 restraints weight = 36883.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148904 restraints weight = 36251.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151009 restraints weight = 25028.044| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3495 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= 0.115 Angle : 0.504 6.607 11113 Z= 0.263 Chirality : 0.038 0.141 1257 Planarity : 0.005 0.049 1431 Dihedral : 7.871 165.632 1094 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -1.10 (0.77), residues: 47 loop : 0.22 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 56 HIS 0.004 0.001 HIS B 279 PHE 0.013 0.001 PHE B 479 TYR 0.009 0.001 TYR B 241 ARG 0.002 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 419) hydrogen bonds : angle 4.96332 ( 1221) covalent geometry : bond 0.00249 ( 8182) covalent geometry : angle 0.50357 (11113) Misc. bond : bond 0.00007 ( 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 133 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 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: B 81 LEU cc_start: 0.5974 (mm) cc_final: 0.5650 (mm) REVERT: B 90 ASN cc_start: 0.8325 (t0) cc_final: 0.7691 (p0) REVERT: B 92 ASN cc_start: 0.7958 (t0) cc_final: 0.7671 (t0) REVERT: B 114 MET cc_start: 0.7245 (mmt) cc_final: 0.6643 (mmt) REVERT: B 159 VAL cc_start: 0.8759 (m) cc_final: 0.8546 (p) REVERT: B 163 MET cc_start: 0.5690 (ptm) cc_final: 0.5387 (ptm) REVERT: B 209 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7696 (mm-40) REVERT: B 646 GLN cc_start: 0.6726 (mt0) cc_final: 0.6260 (mt0) REVERT: B 718 MET cc_start: 0.5343 (tpp) cc_final: 0.4796 (tpp) REVERT: B 767 PHE cc_start: 0.8252 (m-80) cc_final: 0.7937 (m-10) REVERT: C 75 THR cc_start: 0.7106 (m) cc_final: 0.6742 (m) REVERT: C 119 LEU cc_start: 0.7681 (mm) cc_final: 0.7393 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4293 time to fit residues: 78.3111 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 : 1.156 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.178678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144582 restraints weight = 36409.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151656 restraints weight = 38508.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152189 restraints weight = 18867.957| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8184 Z= 0.136 Angle : 0.524 6.828 11113 Z= 0.275 Chirality : 0.038 0.141 1257 Planarity : 0.004 0.050 1431 Dihedral : 7.908 163.382 1094 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: 0.70 (0.27), residues: 1001 helix: 0.98 (0.21), residues: 586 sheet: -1.49 (0.73), residues: 48 loop : 0.10 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 56 HIS 0.005 0.001 HIS B 252 PHE 0.017 0.001 PHE B 479 TYR 0.014 0.001 TYR B 288 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 419) hydrogen bonds : angle 5.01833 ( 1221) covalent geometry : bond 0.00298 ( 8182) covalent geometry : angle 0.52427 (11113) Misc. bond : bond 0.00006 ( 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 130 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.251 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: 0.8353 (t0) cc_final: 0.7780 (p0) REVERT: B 92 ASN cc_start: 0.7933 (t0) cc_final: 0.7677 (t0) REVERT: B 159 VAL cc_start: 0.8713 (m) cc_final: 0.8481 (p) REVERT: B 163 MET cc_start: 0.5802 (ptm) cc_final: 0.5561 (ptm) REVERT: B 209 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7854 (mm-40) REVERT: B 467 MET cc_start: 0.4584 (ptt) cc_final: 0.4371 (ptt) REVERT: B 646 GLN cc_start: 0.6785 (mt0) cc_final: 0.6329 (mt0) REVERT: B 718 MET cc_start: 0.5430 (tpp) cc_final: 0.4861 (tpp) REVERT: B 742 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 743 LEU cc_start: 0.9048 (mm) cc_final: 0.8577 (mm) REVERT: B 767 PHE cc_start: 0.8289 (m-80) cc_final: 0.7955 (m-10) REVERT: C 75 THR cc_start: 0.7411 (m) cc_final: 0.6809 (m) REVERT: C 119 LEU cc_start: 0.7622 (mm) cc_final: 0.7353 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4290 time to fit residues: 78.8380 Evaluate side-chains 108 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 0.0060 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.174757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.138198 restraints weight = 37386.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139485 restraints weight = 22428.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140644 restraints weight = 18353.207| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8184 Z= 0.105 Angle : 0.494 6.432 11113 Z= 0.257 Chirality : 0.037 0.136 1257 Planarity : 0.004 0.049 1431 Dihedral : 7.651 158.918 1094 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 1.20 (0.21), residues: 580 sheet: -1.45 (0.74), residues: 48 loop : 0.25 (0.36), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 56 HIS 0.004 0.001 HIS B 503 PHE 0.007 0.001 PHE B 256 TYR 0.008 0.001 TYR B 120 ARG 0.001 0.000 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 419) hydrogen bonds : angle 4.82092 ( 1221) covalent geometry : bond 0.00231 ( 8182) covalent geometry : angle 0.49392 (11113) Misc. bond : bond 0.00004 ( 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 129 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.239 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: B 90 ASN cc_start: 0.8459 (t0) cc_final: 0.7801 (p0) REVERT: B 92 ASN cc_start: 0.8020 (t0) cc_final: 0.7748 (t0) REVERT: B 159 VAL cc_start: 0.8818 (m) cc_final: 0.8565 (p) REVERT: B 209 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7826 (mm-40) REVERT: B 646 GLN cc_start: 0.6898 (mt0) cc_final: 0.6474 (mt0) REVERT: B 718 MET cc_start: 0.5429 (tpp) cc_final: 0.4848 (tpp) REVERT: B 742 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8287 (tm-30) REVERT: B 743 LEU cc_start: 0.9224 (mm) cc_final: 0.8820 (mm) REVERT: B 767 PHE cc_start: 0.8333 (m-80) cc_final: 0.7912 (m-10) REVERT: C 75 THR cc_start: 0.7276 (m) cc_final: 0.6670 (m) REVERT: C 119 LEU cc_start: 0.7710 (mm) cc_final: 0.7465 (mt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4110 time to fit residues: 73.7961 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 : 1.260 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 73 optimal weight: 0.0670 chunk 79 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ** 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 = 0.4338 r_free = 0.4338 target = 0.174697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138416 restraints weight = 37819.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138975 restraints weight = 24495.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140829 restraints weight = 19878.741| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.4030 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= 0.105 Angle : 0.494 6.493 11113 Z= 0.257 Chirality : 0.037 0.137 1257 Planarity : 0.004 0.055 1431 Dihedral : 7.572 157.245 1094 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.03 (0.27), residues: 1001 helix: 1.26 (0.21), residues: 580 sheet: -1.48 (0.74), residues: 48 loop : 0.23 (0.36), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 56 HIS 0.007 0.001 HIS B 207 PHE 0.007 0.001 PHE B 256 TYR 0.007 0.001 TYR B 288 ARG 0.005 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 419) hydrogen bonds : angle 4.77698 ( 1221) covalent geometry : bond 0.00230 ( 8182) covalent geometry : angle 0.49373 (11113) Misc. bond : bond 0.00003 ( 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 125 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.160 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: B 90 ASN cc_start: 0.8464 (t0) cc_final: 0.7804 (p0) REVERT: B 92 ASN cc_start: 0.8010 (t0) cc_final: 0.7742 (t0) REVERT: B 159 VAL cc_start: 0.8905 (m) cc_final: 0.8654 (p) REVERT: B 209 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7810 (mm-40) REVERT: B 646 GLN cc_start: 0.6893 (mt0) cc_final: 0.6514 (mt0) REVERT: B 718 MET cc_start: 0.5435 (tpp) cc_final: 0.4846 (tpp) REVERT: B 742 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 743 LEU cc_start: 0.9188 (mm) cc_final: 0.8754 (mm) REVERT: B 767 PHE cc_start: 0.8344 (m-80) cc_final: 0.7937 (m-10) REVERT: C 75 THR cc_start: 0.7219 (m) cc_final: 0.6621 (m) REVERT: C 119 LEU cc_start: 0.7723 (mm) cc_final: 0.7488 (mt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3969 time to fit residues: 69.4338 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 : 1.304 ------------------------------------------------------------------------------- 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: 0.6980 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** C 141 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 = 0.4366 r_free = 0.4366 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.145317 restraints weight = 36650.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143557 restraints weight = 36752.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.146856 restraints weight = 28441.303| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8184 Z= 0.143 Angle : 0.531 6.988 11113 Z= 0.280 Chirality : 0.038 0.138 1257 Planarity : 0.005 0.055 1431 Dihedral : 7.758 156.663 1094 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.78 (0.27), residues: 1001 helix: 1.09 (0.21), residues: 584 sheet: -1.71 (0.74), residues: 48 loop : 0.08 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 56 HIS 0.006 0.001 HIS B 207 PHE 0.010 0.001 PHE B 256 TYR 0.012 0.001 TYR B 202 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 419) hydrogen bonds : angle 4.96585 ( 1221) covalent geometry : bond 0.00316 ( 8182) covalent geometry : angle 0.53077 (11113) Misc. bond : bond 0.00008 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.57 seconds wall clock time: 86 minutes 2.87 seconds (5162.87 seconds total)