Starting phenix.real_space_refine on Sun Jul 21 23:53:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/07_2024/8q0n_18056_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/07_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_18056/07_2024/8q0n_18056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/07_2024/8q0n_18056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/07_2024/8q0n_18056_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/07_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.00, per 1000 atoms: 0.50 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: 13.17 Conformation dependent library (CDL) restraints added in 1.8 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: 1.41 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: 5.94 Time building geometry restraints manager: 13.85 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 1.850 nonbonded pdb=" OD1 ASP C 11 " pdb=" HE1 TRP C 97 " model vdw 1.647 1.850 nonbonded pdb=" OD1 ASP C 65 " pdb="HH22 ARG C 68 " model vdw 1.667 1.850 nonbonded pdb=" OE1 GLN B 756 " pdb=" H GLN B 756 " model vdw 1.677 1.850 nonbonded pdb=" H THR B 733 " pdb=" OD1 ASN B 736 " model vdw 1.680 1.850 ... (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 ========== 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: 1.190 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: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 54.250 Find NCS groups from input model: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.790 ------------------------------------------------------------------------------- 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 : 1.238 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: 0.4642 time to fit residues: 96.2031 Evaluate side-chains 128 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 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 ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8182 Z= 0.242 Angle : 0.583 7.860 11113 Z= 0.313 Chirality : 0.040 0.137 1257 Planarity : 0.004 0.052 1431 Dihedral : 7.818 163.490 1094 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 0.87 (0.26), residues: 1001 helix: 0.91 (0.21), residues: 586 sheet: 0.47 (0.75), residues: 44 loop : 0.25 (0.34), residues: 371 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 0.012 0.002 PHE B 563 TYR 0.014 0.002 TYR B 202 ARG 0.002 0.000 ARG C 102 *********************** 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 139 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.297 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: B 90 ASN cc_start: 0.7462 (t0) cc_final: 0.7148 (t0) REVERT: B 243 GLU cc_start: 0.2339 (tp30) cc_final: 0.1983 (tp30) REVERT: B 312 ASN cc_start: 0.9108 (t0) cc_final: 0.8827 (t0) REVERT: B 313 TYR cc_start: 0.8083 (p90) cc_final: 0.7755 (p90) REVERT: B 447 MET cc_start: 0.9194 (mmp) cc_final: 0.8924 (mmm) REVERT: B 646 GLN cc_start: 0.5622 (mt0) cc_final: 0.5242 (mt0) REVERT: B 718 MET cc_start: 0.5345 (tpp) cc_final: 0.5045 (tpp) REVERT: B 846 PHE cc_start: 0.4911 (m-80) cc_final: 0.4592 (m-80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.3984 time to fit residues: 78.2991 Evaluate side-chains 118 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.4473 moved from start: 0.2310 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= 0.205 Angle : 0.541 7.029 11113 Z= 0.288 Chirality : 0.039 0.152 1257 Planarity : 0.004 0.047 1431 Dihedral : 8.200 178.145 1094 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 0.74 (0.27), residues: 1001 helix: 0.86 (0.21), residues: 584 sheet: -0.09 (0.74), residues: 48 loop : 0.19 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.006 0.001 HIS B 252 PHE 0.016 0.002 PHE B 459 TYR 0.011 0.002 TYR B 202 ARG 0.004 0.000 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 134 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.284 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: 0.7514 (t0) cc_final: 0.6819 (p0) REVERT: B 159 VAL cc_start: 0.6305 (t) cc_final: 0.6013 (m) REVERT: B 312 ASN cc_start: 0.9098 (t0) cc_final: 0.8797 (t0) REVERT: B 313 TYR cc_start: 0.8111 (p90) cc_final: 0.7757 (p90) REVERT: B 447 MET cc_start: 0.9129 (mmp) cc_final: 0.8883 (mmm) REVERT: B 646 GLN cc_start: 0.5269 (mt0) cc_final: 0.4961 (mt0) REVERT: B 718 MET cc_start: 0.5423 (tpp) cc_final: 0.5126 (tpp) REVERT: B 767 PHE cc_start: 0.7122 (m-80) cc_final: 0.6535 (m-10) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3774 time to fit residues: 72.1556 Evaluate side-chains 112 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.2633 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= 0.177 Angle : 0.513 6.815 11113 Z= 0.270 Chirality : 0.037 0.141 1257 Planarity : 0.005 0.091 1431 Dihedral : 8.118 177.428 1094 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 0.71 (0.27), residues: 1001 helix: 0.80 (0.21), residues: 591 sheet: -0.03 (0.76), residues: 48 loop : 0.22 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 364 HIS 0.005 0.001 HIS B 637 PHE 0.015 0.001 PHE B 502 TYR 0.009 0.001 TYR B 202 ARG 0.002 0.000 ARG C 94 *********************** 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 133 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.278 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: 0.7502 (t0) cc_final: 0.6800 (p0) REVERT: B 159 VAL cc_start: 0.6413 (t) cc_final: 0.6089 (m) REVERT: B 312 ASN cc_start: 0.9055 (t0) cc_final: 0.8746 (t0) REVERT: B 313 TYR cc_start: 0.8110 (p90) cc_final: 0.7720 (p90) REVERT: B 361 GLU cc_start: 0.9248 (pt0) cc_final: 0.8938 (tp30) REVERT: B 447 MET cc_start: 0.9111 (mmp) cc_final: 0.8867 (mmm) REVERT: B 634 ASN cc_start: 0.7768 (t0) cc_final: 0.7563 (t0) REVERT: B 646 GLN cc_start: 0.5186 (mt0) cc_final: 0.4888 (mt0) REVERT: B 718 MET cc_start: 0.5457 (tpp) cc_final: 0.5157 (tpp) REVERT: B 767 PHE cc_start: 0.7132 (m-80) cc_final: 0.6535 (m-10) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3650 time to fit residues: 69.5767 Evaluate side-chains 112 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4525 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8182 Z= 0.337 Angle : 0.659 8.172 11113 Z= 0.360 Chirality : 0.041 0.174 1257 Planarity : 0.005 0.056 1431 Dihedral : 8.957 176.056 1094 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.12 (0.26), residues: 1001 helix: 0.28 (0.21), residues: 579 sheet: -1.67 (0.68), residues: 50 loop : -0.19 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 56 HIS 0.012 0.002 HIS B 252 PHE 0.022 0.003 PHE B 256 TYR 0.020 0.002 TYR B 288 ARG 0.006 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 129 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.362 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: 0.7681 (t0) cc_final: 0.6960 (p0) REVERT: B 243 GLU cc_start: 0.3846 (tp30) cc_final: 0.3519 (tp30) REVERT: B 447 MET cc_start: 0.9156 (mmp) cc_final: 0.8929 (mmm) REVERT: B 718 MET cc_start: 0.5467 (tpp) cc_final: 0.5169 (tpp) REVERT: B 767 PHE cc_start: 0.7132 (m-80) cc_final: 0.6514 (m-10) REVERT: B 848 ASN cc_start: 0.5669 (t0) cc_final: 0.5339 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3906 time to fit residues: 70.7830 Evaluate side-chains 112 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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: 0.6980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 594 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: 0.4470 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8182 Z= 0.163 Angle : 0.524 6.645 11113 Z= 0.274 Chirality : 0.038 0.137 1257 Planarity : 0.004 0.052 1431 Dihedral : 8.130 166.628 1094 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.40 (0.27), residues: 1001 helix: 0.67 (0.21), residues: 592 sheet: -1.14 (0.72), residues: 49 loop : 0.01 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 56 HIS 0.005 0.001 HIS B 279 PHE 0.013 0.001 PHE B 479 TYR 0.013 0.001 TYR B 288 ARG 0.003 0.000 ARG B 353 *********************** 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 133 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.257 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: 0.7628 (t0) cc_final: 0.6889 (p0) REVERT: B 243 GLU cc_start: 0.3710 (tp30) cc_final: 0.3388 (tp30) REVERT: B 312 ASN cc_start: 0.9066 (t0) cc_final: 0.8800 (t0) REVERT: B 313 TYR cc_start: 0.8084 (p90) cc_final: 0.7719 (p90) REVERT: B 361 GLU cc_start: 0.9184 (pt0) cc_final: 0.8896 (tp30) REVERT: B 447 MET cc_start: 0.9128 (mmp) cc_final: 0.8874 (mmm) REVERT: B 630 ASN cc_start: 0.9252 (t0) cc_final: 0.8763 (m110) REVERT: B 634 ASN cc_start: 0.7923 (t0) cc_final: 0.7628 (t0) REVERT: B 646 GLN cc_start: 0.5210 (mt0) cc_final: 0.4916 (mt0) REVERT: B 718 MET cc_start: 0.5417 (tpp) cc_final: 0.5123 (tpp) REVERT: B 767 PHE cc_start: 0.7125 (m-80) cc_final: 0.6414 (m-10) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4244 time to fit residues: 77.5671 Evaluate side-chains 109 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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: 0.4472 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8182 Z= 0.157 Angle : 0.506 6.695 11113 Z= 0.264 Chirality : 0.037 0.139 1257 Planarity : 0.004 0.050 1431 Dihedral : 8.009 165.948 1094 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 0.62 (0.27), residues: 1001 helix: 0.89 (0.21), residues: 592 sheet: -1.23 (0.73), residues: 50 loop : 0.06 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 56 HIS 0.004 0.001 HIS B 637 PHE 0.012 0.001 PHE B 479 TYR 0.009 0.001 TYR B 288 ARG 0.002 0.000 ARG C 102 *********************** 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 129 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.238 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: 0.7582 (t0) cc_final: 0.6833 (p0) REVERT: B 243 GLU cc_start: 0.3369 (tp30) cc_final: 0.3069 (tp30) REVERT: B 312 ASN cc_start: 0.9080 (t0) cc_final: 0.8812 (t0) REVERT: B 313 TYR cc_start: 0.8060 (p90) cc_final: 0.7689 (p90) REVERT: B 361 GLU cc_start: 0.9166 (pt0) cc_final: 0.8904 (tp30) REVERT: B 447 MET cc_start: 0.9119 (mmp) cc_final: 0.8880 (mmm) REVERT: B 630 ASN cc_start: 0.9260 (t0) cc_final: 0.8795 (m110) REVERT: B 634 ASN cc_start: 0.7908 (t0) cc_final: 0.7606 (t0) REVERT: B 718 MET cc_start: 0.5433 (tpp) cc_final: 0.5129 (tpp) REVERT: B 767 PHE cc_start: 0.7069 (m-80) cc_final: 0.6488 (m-10) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3909 time to fit residues: 70.8434 Evaluate side-chains 104 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.0040 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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: 0.4476 moved from start: 0.3843 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= 0.178 Angle : 0.520 6.868 11113 Z= 0.274 Chirality : 0.038 0.139 1257 Planarity : 0.004 0.049 1431 Dihedral : 8.009 163.806 1094 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: 0.89 (0.21), residues: 589 sheet: -1.29 (0.63), residues: 62 loop : 0.02 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 56 HIS 0.008 0.001 HIS B 207 PHE 0.019 0.001 PHE B 858 TYR 0.010 0.001 TYR B 288 ARG 0.002 0.000 ARG B 353 *********************** 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 126 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.312 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: 0.7574 (t0) cc_final: 0.6828 (p0) REVERT: B 312 ASN cc_start: 0.9071 (t0) cc_final: 0.8803 (t0) REVERT: B 313 TYR cc_start: 0.8085 (p90) cc_final: 0.7736 (p90) REVERT: B 361 GLU cc_start: 0.9167 (pt0) cc_final: 0.8860 (tp30) REVERT: B 447 MET cc_start: 0.9125 (mmp) cc_final: 0.8887 (mmm) REVERT: B 630 ASN cc_start: 0.9271 (t0) cc_final: 0.8781 (m110) REVERT: B 634 ASN cc_start: 0.7870 (t0) cc_final: 0.7575 (t0) REVERT: B 718 MET cc_start: 0.5427 (tpp) cc_final: 0.5126 (tpp) REVERT: B 767 PHE cc_start: 0.7083 (m-80) cc_final: 0.6547 (m-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4168 time to fit residues: 72.8084 Evaluate side-chains 104 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 450 ASN ** 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: 0.4473 moved from start: 0.3933 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= 0.154 Angle : 0.501 6.734 11113 Z= 0.262 Chirality : 0.037 0.139 1257 Planarity : 0.004 0.047 1431 Dihedral : 7.902 162.798 1094 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.73 (0.27), residues: 1001 helix: 1.01 (0.21), residues: 590 sheet: -1.50 (0.72), residues: 50 loop : 0.11 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 56 HIS 0.004 0.001 HIS B 637 PHE 0.012 0.001 PHE B 858 TYR 0.008 0.001 TYR B 288 ARG 0.004 0.000 ARG B 107 *********************** 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 : 1.259 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: B 90 ASN cc_start: 0.7523 (t0) cc_final: 0.6775 (p0) REVERT: B 312 ASN cc_start: 0.9057 (t0) cc_final: 0.8803 (t0) REVERT: B 313 TYR cc_start: 0.8077 (p90) cc_final: 0.7742 (p90) REVERT: B 355 GLN cc_start: 0.9175 (mt0) cc_final: 0.8776 (mm110) REVERT: B 361 GLU cc_start: 0.9149 (pt0) cc_final: 0.8838 (tp30) REVERT: B 447 MET cc_start: 0.9118 (mmp) cc_final: 0.8881 (mmm) REVERT: B 630 ASN cc_start: 0.9283 (t0) cc_final: 0.8801 (m110) REVERT: B 634 ASN cc_start: 0.7844 (t0) cc_final: 0.7556 (t0) REVERT: B 718 MET cc_start: 0.5393 (tpp) cc_final: 0.5095 (tpp) REVERT: B 767 PHE cc_start: 0.7080 (m-80) cc_final: 0.6574 (m-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3861 time to fit residues: 68.8017 Evaluate side-chains 104 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.4501 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8182 Z= 0.224 Angle : 0.564 7.109 11113 Z= 0.300 Chirality : 0.039 0.148 1257 Planarity : 0.004 0.050 1431 Dihedral : 8.327 167.866 1094 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: 0.39 (0.27), residues: 1001 helix: 0.87 (0.21), residues: 579 sheet: -1.68 (0.61), residues: 62 loop : -0.22 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 56 HIS 0.006 0.001 HIS B 207 PHE 0.014 0.002 PHE B 858 TYR 0.012 0.002 TYR B 288 ARG 0.003 0.000 ARG B 664 ********************** 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 123 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.284 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: B 90 ASN cc_start: 0.7672 (t0) cc_final: 0.6977 (p0) REVERT: B 312 ASN cc_start: 0.9014 (t0) cc_final: 0.8785 (t0) REVERT: B 361 GLU cc_start: 0.9161 (pt0) cc_final: 0.8835 (tp30) REVERT: B 447 MET cc_start: 0.9127 (mmp) cc_final: 0.8901 (mmm) REVERT: B 630 ASN cc_start: 0.9300 (t0) cc_final: 0.8826 (m110) REVERT: B 634 ASN cc_start: 0.7860 (t0) cc_final: 0.7566 (t0) REVERT: B 718 MET cc_start: 0.5437 (tpp) cc_final: 0.5135 (tpp) REVERT: B 767 PHE cc_start: 0.7065 (m-80) cc_final: 0.6631 (m-10) REVERT: B 848 ASN cc_start: 0.5736 (t0) cc_final: 0.5444 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4362 time to fit residues: 74.1881 Evaluate side-chains 107 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 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 73 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145258 restraints weight = 36923.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.150373 restraints weight = 39672.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.151644 restraints weight = 22151.767| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4362 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= 0.171 Angle : 0.518 6.793 11113 Z= 0.272 Chirality : 0.038 0.138 1257 Planarity : 0.004 0.053 1431 Dihedral : 8.189 167.975 1094 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: 0.66 (0.27), residues: 1001 helix: 1.07 (0.21), residues: 574 sheet: -1.70 (0.73), residues: 49 loop : -0.08 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.005 0.001 HIS B 637 PHE 0.014 0.001 PHE B 327 TYR 0.007 0.001 TYR B 202 ARG 0.008 0.000 ARG B 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.83 seconds wall clock time: 64 minutes 15.28 seconds (3855.28 seconds total)