Starting phenix.real_space_refine on Tue Aug 6 10:49:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_18056_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_18056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_18056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_18056_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/08_2024/8q0n_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 Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.71, 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 - 3.50 Amino acid : False - 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: 12.45 Conformation dependent library (CDL) restraints added in 1.7 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: 5.59 Time building geometry restraints manager: 13.04 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: 100.25 - 107.00: 334 107.00 - 113.75: 19118 113.75 - 120.50: 5392 120.50 - 127.25: 4153 127.25 - 134.00: 104 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: 2.020 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: 0.240 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 51.610 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- 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 : 0.002 0.034 8182 Z= 0.136 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.791 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: 0.4324 time to fit residues: 89.9777 Evaluate side-chains 128 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4457 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 8182 Z= 0.251 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.108 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 243 GLU cc_start: 0.2309 (tp30) cc_final: 0.1939 (tp30) REVERT: B 312 ASN cc_start: 0.9111 (t0) cc_final: 0.8827 (t0) REVERT: B 313 TYR cc_start: 0.8083 (p90) cc_final: 0.7746 (p90) REVERT: B 447 MET cc_start: 0.9188 (mmp) cc_final: 0.8916 (mmm) REVERT: B 646 GLN cc_start: 0.5618 (mt0) cc_final: 0.5238 (mt0) REVERT: B 718 MET cc_start: 0.5354 (tpp) cc_final: 0.5052 (tpp) REVERT: B 846 PHE cc_start: 0.4951 (m-80) cc_final: 0.4630 (m-80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4338 time to fit residues: 85.4322 Evaluate side-chains 115 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4474 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8182 Z= 0.225 Angle : 0.554 7.142 11113 Z= 0.296 Chirality : 0.039 0.154 1257 Planarity : 0.005 0.058 1431 Dihedral : 8.301 177.853 1094 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 0.68 (0.27), residues: 1001 helix: 0.85 (0.21), residues: 584 sheet: -0.43 (0.74), residues: 48 loop : 0.13 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.007 0.001 HIS B 252 PHE 0.015 0.002 PHE B 459 TYR 0.011 0.002 TYR B 202 ARG 0.004 0.001 ARG B 475 *********************** 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 133 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 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: B 90 ASN cc_start: 0.7679 (t0) cc_final: 0.7001 (p0) REVERT: B 159 VAL cc_start: 0.6355 (t) cc_final: 0.6053 (m) REVERT: B 312 ASN cc_start: 0.9111 (t0) cc_final: 0.8813 (t0) REVERT: B 313 TYR cc_start: 0.8063 (p90) cc_final: 0.7714 (p90) REVERT: B 447 MET cc_start: 0.9123 (mmp) cc_final: 0.8873 (mmm) REVERT: B 646 GLN cc_start: 0.5297 (mt0) cc_final: 0.5029 (mt0) REVERT: B 718 MET cc_start: 0.5390 (tpp) cc_final: 0.5089 (tpp) REVERT: B 767 PHE cc_start: 0.7119 (m-80) cc_final: 0.6521 (m-10) REVERT: C 75 THR cc_start: 0.5253 (m) cc_final: 0.5000 (m) REVERT: C 165 LEU cc_start: 0.6865 (tp) cc_final: 0.6573 (tp) REVERT: C 166 LYS cc_start: 0.8028 (mttm) cc_final: 0.7316 (tptt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3844 time to fit residues: 71.9384 Evaluate side-chains 109 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 overall best weight: 0.8724 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4458 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8182 Z= 0.180 Angle : 0.520 6.889 11113 Z= 0.275 Chirality : 0.038 0.139 1257 Planarity : 0.005 0.102 1431 Dihedral : 8.133 175.090 1094 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1001 helix: 0.83 (0.21), residues: 591 sheet: -0.46 (0.76), residues: 48 loop : 0.22 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 364 HIS 0.004 0.001 HIS B 279 PHE 0.014 0.001 PHE B 459 TYR 0.015 0.001 TYR B 241 ARG 0.003 0.000 ARG B 527 *********************** 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 132 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.452 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: 0.7671 (t0) cc_final: 0.6992 (p0) REVERT: B 159 VAL cc_start: 0.6406 (t) cc_final: 0.6087 (m) REVERT: B 312 ASN cc_start: 0.9097 (t0) cc_final: 0.8806 (t0) REVERT: B 313 TYR cc_start: 0.8076 (p90) cc_final: 0.7692 (p90) REVERT: B 355 GLN cc_start: 0.9092 (mt0) cc_final: 0.8865 (mt0) REVERT: B 447 MET cc_start: 0.9109 (mmp) cc_final: 0.8857 (mmm) REVERT: B 634 ASN cc_start: 0.7869 (t0) cc_final: 0.7651 (t0) REVERT: B 646 GLN cc_start: 0.5338 (mt0) cc_final: 0.5066 (mt0) REVERT: B 718 MET cc_start: 0.5452 (tpp) cc_final: 0.5149 (tpp) REVERT: B 767 PHE cc_start: 0.7084 (m-80) cc_final: 0.6453 (m-10) REVERT: C 165 LEU cc_start: 0.6860 (tp) cc_final: 0.6552 (tp) REVERT: C 166 LYS cc_start: 0.8020 (mttm) cc_final: 0.7299 (tptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3624 time to fit residues: 68.0038 Evaluate side-chains 109 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4503 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8182 Z= 0.284 Angle : 0.611 7.694 11113 Z= 0.332 Chirality : 0.041 0.152 1257 Planarity : 0.005 0.070 1431 Dihedral : 8.789 173.300 1094 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.09 (0.26), residues: 1001 helix: 0.37 (0.21), residues: 588 sheet: -1.14 (0.73), residues: 48 loop : -0.05 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 364 HIS 0.010 0.002 HIS B 252 PHE 0.019 0.002 PHE B 256 TYR 0.019 0.002 TYR B 288 ARG 0.005 0.001 ARG C 68 *********************** 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 126 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.293 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: 0.7736 (t0) cc_final: 0.7029 (p0) REVERT: B 312 ASN cc_start: 0.9074 (t0) cc_final: 0.8799 (t0) REVERT: B 313 TYR cc_start: 0.8188 (p90) cc_final: 0.7761 (p90) REVERT: B 447 MET cc_start: 0.9135 (mmp) cc_final: 0.8887 (mmm) REVERT: B 634 ASN cc_start: 0.8005 (t0) cc_final: 0.7750 (t0) REVERT: B 646 GLN cc_start: 0.5280 (mt0) cc_final: 0.4992 (mt0) REVERT: B 718 MET cc_start: 0.5453 (tpp) cc_final: 0.5157 (tpp) REVERT: B 767 PHE cc_start: 0.7132 (m-80) cc_final: 0.6408 (m-10) REVERT: B 848 ASN cc_start: 0.5488 (t0) cc_final: 0.5148 (t0) REVERT: C 75 THR cc_start: 0.5271 (m) cc_final: 0.5016 (m) REVERT: C 165 LEU cc_start: 0.6923 (tp) cc_final: 0.6616 (tp) REVERT: C 166 LYS cc_start: 0.7926 (mttm) cc_final: 0.7240 (tptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4365 time to fit residues: 77.2148 Evaluate side-chains 106 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4461 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8182 Z= 0.155 Angle : 0.517 6.473 11113 Z= 0.271 Chirality : 0.038 0.139 1257 Planarity : 0.004 0.051 1431 Dihedral : 8.048 162.022 1094 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % 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: 0.53 (0.27), residues: 1001 helix: 0.78 (0.21), residues: 583 sheet: -1.10 (0.77), residues: 47 loop : 0.07 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 279 PHE 0.013 0.001 PHE B 502 TYR 0.010 0.001 TYR B 460 ARG 0.002 0.000 ARG B 107 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.331 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: 0.7661 (t0) cc_final: 0.6916 (p0) REVERT: B 312 ASN cc_start: 0.9087 (t0) cc_final: 0.8812 (t0) REVERT: B 313 TYR cc_start: 0.8129 (p90) cc_final: 0.7680 (p90) REVERT: B 355 GLN cc_start: 0.9077 (mt0) cc_final: 0.8857 (mt0) REVERT: B 361 GLU cc_start: 0.9174 (pt0) cc_final: 0.8881 (tp30) REVERT: B 447 MET cc_start: 0.9118 (mmp) cc_final: 0.8868 (mmm) REVERT: B 630 ASN cc_start: 0.9262 (t0) cc_final: 0.8789 (m110) REVERT: B 634 ASN cc_start: 0.8059 (t0) cc_final: 0.7779 (t0) REVERT: B 646 GLN cc_start: 0.5305 (mt0) cc_final: 0.5035 (mt0) REVERT: B 718 MET cc_start: 0.5435 (tpp) cc_final: 0.5137 (tpp) REVERT: B 767 PHE cc_start: 0.7105 (m-80) cc_final: 0.6437 (m-10) REVERT: C 75 THR cc_start: 0.5169 (m) cc_final: 0.4935 (m) REVERT: C 165 LEU cc_start: 0.6909 (tp) cc_final: 0.6569 (tp) REVERT: C 166 LYS cc_start: 0.8005 (mttm) cc_final: 0.7303 (tptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4695 time to fit residues: 84.8765 Evaluate side-chains 105 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4469 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8182 Z= 0.166 Angle : 0.514 6.518 11113 Z= 0.269 Chirality : 0.038 0.141 1257 Planarity : 0.004 0.052 1431 Dihedral : 8.004 162.063 1094 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: 0.64 (0.27), residues: 1001 helix: 0.92 (0.21), residues: 583 sheet: -1.32 (0.76), residues: 47 loop : 0.04 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 364 HIS 0.005 0.001 HIS B 207 PHE 0.012 0.001 PHE B 479 TYR 0.007 0.001 TYR B 288 ARG 0.002 0.000 ARG B 274 *********************** 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 131 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.351 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: 0.7658 (t0) cc_final: 0.6918 (p0) REVERT: B 312 ASN cc_start: 0.9049 (t0) cc_final: 0.8779 (t0) REVERT: B 313 TYR cc_start: 0.8154 (p90) cc_final: 0.7717 (p90) REVERT: B 355 GLN cc_start: 0.9081 (mt0) cc_final: 0.8861 (mt0) REVERT: B 361 GLU cc_start: 0.9167 (pt0) cc_final: 0.8878 (tp30) REVERT: B 447 MET cc_start: 0.9120 (mmp) cc_final: 0.8867 (mmm) REVERT: B 630 ASN cc_start: 0.9266 (t0) cc_final: 0.8806 (m110) REVERT: B 634 ASN cc_start: 0.8062 (t0) cc_final: 0.7782 (t0) REVERT: B 646 GLN cc_start: 0.5209 (mt0) cc_final: 0.4973 (mt0) REVERT: B 718 MET cc_start: 0.5456 (tpp) cc_final: 0.5159 (tpp) REVERT: B 767 PHE cc_start: 0.7102 (m-80) cc_final: 0.6418 (m-10) REVERT: C 75 THR cc_start: 0.5043 (m) cc_final: 0.4778 (m) REVERT: C 165 LEU cc_start: 0.6913 (tp) cc_final: 0.6569 (tp) REVERT: C 166 LYS cc_start: 0.7938 (mttm) cc_final: 0.7237 (tptt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4240 time to fit residues: 76.6690 Evaluate side-chains 112 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4490 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8182 Z= 0.218 Angle : 0.555 6.985 11113 Z= 0.296 Chirality : 0.039 0.140 1257 Planarity : 0.005 0.052 1431 Dihedral : 8.147 160.666 1094 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.44 (0.27), residues: 1001 helix: 0.84 (0.21), residues: 586 sheet: -1.71 (0.74), residues: 48 loop : -0.15 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 693 HIS 0.007 0.001 HIS B 279 PHE 0.011 0.002 PHE B 256 TYR 0.012 0.001 TYR B 288 ARG 0.002 0.000 ARG C 68 *********************** 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 133 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.225 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: 0.7695 (t0) cc_final: 0.6970 (p0) REVERT: B 312 ASN cc_start: 0.9046 (t0) cc_final: 0.8822 (t0) REVERT: B 313 TYR cc_start: 0.8250 (p90) cc_final: 0.7943 (p90) REVERT: B 361 GLU cc_start: 0.9170 (pt0) cc_final: 0.8847 (tp30) REVERT: B 447 MET cc_start: 0.9127 (mmp) cc_final: 0.8884 (mmm) REVERT: B 630 ASN cc_start: 0.9283 (t0) cc_final: 0.8803 (m110) REVERT: B 634 ASN cc_start: 0.8049 (t0) cc_final: 0.7778 (t0) REVERT: B 718 MET cc_start: 0.5491 (tpp) cc_final: 0.5189 (tpp) REVERT: B 767 PHE cc_start: 0.7146 (m-80) cc_final: 0.6517 (m-10) REVERT: B 848 ASN cc_start: 0.5562 (t0) cc_final: 0.5303 (t0) REVERT: C 165 LEU cc_start: 0.6933 (tp) cc_final: 0.6599 (tp) REVERT: C 166 LYS cc_start: 0.7965 (mttm) cc_final: 0.7258 (tptt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4204 time to fit residues: 76.8235 Evaluate side-chains 112 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4468 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8182 Z= 0.169 Angle : 0.516 6.614 11113 Z= 0.271 Chirality : 0.038 0.140 1257 Planarity : 0.004 0.054 1431 Dihedral : 7.886 155.612 1094 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.27), residues: 1001 helix: 1.05 (0.21), residues: 581 sheet: -1.63 (0.76), residues: 47 loop : -0.07 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 56 HIS 0.004 0.001 HIS B 279 PHE 0.010 0.001 PHE B 479 TYR 0.008 0.001 TYR B 288 ARG 0.005 0.000 ARG C 66 *********************** 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 126 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.267 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: 0.7674 (t0) cc_final: 0.6967 (p0) REVERT: B 312 ASN cc_start: 0.9034 (t0) cc_final: 0.8814 (t0) REVERT: B 313 TYR cc_start: 0.8233 (p90) cc_final: 0.7928 (p90) REVERT: B 355 GLN cc_start: 0.9088 (mt0) cc_final: 0.8870 (mt0) REVERT: B 361 GLU cc_start: 0.9144 (pt0) cc_final: 0.8829 (tp30) REVERT: B 447 MET cc_start: 0.9120 (mmp) cc_final: 0.8876 (mmm) REVERT: B 530 TRP cc_start: 0.5758 (t60) cc_final: 0.5380 (t60) REVERT: B 630 ASN cc_start: 0.9287 (t0) cc_final: 0.8825 (m110) REVERT: B 634 ASN cc_start: 0.8028 (t0) cc_final: 0.7765 (t0) REVERT: B 718 MET cc_start: 0.5469 (tpp) cc_final: 0.5164 (tpp) REVERT: B 767 PHE cc_start: 0.7020 (m-80) cc_final: 0.6534 (m-10) REVERT: C 165 LEU cc_start: 0.6998 (tp) cc_final: 0.6639 (tp) REVERT: C 166 LYS cc_start: 0.7972 (mttm) cc_final: 0.7261 (tptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4575 time to fit residues: 79.1589 Evaluate side-chains 111 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4467 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8182 Z= 0.159 Angle : 0.507 6.490 11113 Z= 0.265 Chirality : 0.037 0.136 1257 Planarity : 0.005 0.055 1431 Dihedral : 7.749 152.802 1094 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.79 (0.27), residues: 1001 helix: 1.19 (0.21), residues: 581 sheet: -1.67 (0.76), residues: 48 loop : -0.08 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 56 HIS 0.004 0.001 HIS B 329 PHE 0.009 0.001 PHE B 662 TYR 0.008 0.001 TYR B 288 ARG 0.002 0.000 ARG B 66 ********************** 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 127 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.225 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: 0.7641 (t0) cc_final: 0.7020 (p0) REVERT: B 312 ASN cc_start: 0.8990 (t0) cc_final: 0.8780 (t0) REVERT: B 313 TYR cc_start: 0.8237 (p90) cc_final: 0.7912 (p90) REVERT: B 327 PHE cc_start: 0.7045 (t80) cc_final: 0.6804 (t80) REVERT: B 361 GLU cc_start: 0.9142 (pt0) cc_final: 0.8823 (tp30) REVERT: B 447 MET cc_start: 0.9110 (mmp) cc_final: 0.8866 (mmm) REVERT: B 630 ASN cc_start: 0.9297 (t0) cc_final: 0.8863 (m110) REVERT: B 634 ASN cc_start: 0.8050 (t0) cc_final: 0.7787 (t0) REVERT: B 718 MET cc_start: 0.5470 (tpp) cc_final: 0.5163 (tpp) REVERT: B 767 PHE cc_start: 0.6938 (m-80) cc_final: 0.6464 (m-10) REVERT: C 165 LEU cc_start: 0.6988 (tp) cc_final: 0.6604 (tp) REVERT: C 166 LYS cc_start: 0.7980 (mttm) cc_final: 0.7275 (tptt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4282 time to fit residues: 74.5507 Evaluate side-chains 111 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141612 restraints weight = 36952.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145426 restraints weight = 37558.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146791 restraints weight = 24077.780| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8182 Z= 0.234 Angle : 0.560 7.264 11113 Z= 0.298 Chirality : 0.039 0.141 1257 Planarity : 0.005 0.055 1431 Dihedral : 7.968 153.284 1094 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.27), residues: 1001 helix: 1.05 (0.21), residues: 577 sheet: -2.08 (0.73), residues: 48 loop : -0.19 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 56 HIS 0.006 0.001 HIS B 279 PHE 0.013 0.002 PHE B 479 TYR 0.013 0.002 TYR B 202 ARG 0.003 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.22 seconds wall clock time: 64 minutes 40.59 seconds (3880.59 seconds total)