Starting phenix.real_space_refine on Wed Feb 14 20:44:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/02_2024/8f19_28788_updated.pdb" } resolution = 3.49 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= 0.005 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1516 atoms to isotropic. 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 Mg 1 5.21 5 S 37 5.16 5 C 5590 2.51 5 N 1416 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B GLU 177": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8717 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7291 Classifications: {'peptide': 916} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 891} Chain breaks: 3 Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1426 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 171, 'undetermined': 2} Link IDs: {'PTRANS': 6, 'TRANS': 164, None: 2} Not linked: pdbres="VAL B 179 " pdbres="GTP B 201 " Not linked: pdbres="GTP B 201 " pdbres=" MG B 202 " Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8717 At special positions: 0 Unit cell: (92.133, 102.723, 119.667, 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 37 16.00 P 3 15.00 Mg 1 11.99 O 1670 8.00 N 1416 7.00 C 5590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 1 sheets defined 69.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.074A pdb=" N GLN A 11 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.514A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.519A pdb=" N PHE A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.291A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 187 through 206 Processing helix chain 'A' and resid 213 through 235 removed outlier: 4.127A pdb=" N PHE A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 263 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 293 removed outlier: 3.900A pdb=" N ALA A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 323 removed outlier: 4.959A pdb=" N THR A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.775A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 385 through 401 removed outlier: 3.722A pdb=" N LYS A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.562A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 453 through 469 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 498 through 512 Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 523 through 543 removed outlier: 3.980A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 562 removed outlier: 3.734A pdb=" N TYR A 562 " --> pdb=" O GLN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 586 removed outlier: 3.656A pdb=" N SER A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 Processing helix chain 'A' and resid 611 through 631 removed outlier: 4.081A pdb=" N LYS A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.565A pdb=" N VAL A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 641 through 655 Processing helix chain 'A' and resid 665 through 681 removed outlier: 4.816A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 685 through 701 removed outlier: 3.505A pdb=" N TYR A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Proline residue: A 709 - end of helix removed outlier: 5.578A pdb=" N MET A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 744 removed outlier: 4.592A pdb=" N ASN A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 805 through 819 Processing helix chain 'A' and resid 823 through 839 removed outlier: 3.970A pdb=" N GLU A 828 " --> pdb=" O LYS A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 No H-bonds generated for 'chain 'A' and resid 842 through 845' Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 965 through 977 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 993 through 1002 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 97 through 113 Proline residue: B 104 - end of helix removed outlier: 3.525A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 144 removed outlier: 4.232A pdb=" N THR B 137 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 140 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 141 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 143 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 Processing sheet with id= A, first strand: chain 'B' and resid 147 through 150 removed outlier: 4.063A pdb=" N GLN B 147 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N PHE B 13 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS B 62 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 15 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP B 64 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU B 17 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP B 66 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1509 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: 2.93 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2807 1.34 - 1.46: 1789 1.46 - 1.58: 4212 1.58 - 1.69: 5 1.69 - 1.81: 54 Bond restraints: 8867 Sorted by residual: bond pdb=" C2 GTP B 201 " pdb=" N3 GTP B 201 " ideal model delta sigma weight residual 1.380 1.333 0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" N LYS B 125 " pdb=" CA LYS B 125 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.45e-02 4.76e+03 4.98e+00 bond pdb=" N ASP A 665 " pdb=" CA ASP A 665 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.73e+00 bond pdb=" C8 GTP B 201 " pdb=" N7 GTP B 201 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C4' GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 3.96e+00 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.81: 174 106.81 - 113.60: 5023 113.60 - 120.39: 3460 120.39 - 127.18: 3295 127.18 - 133.96: 67 Bond angle restraints: 12019 Sorted by residual: angle pdb=" CA TYR A 513 " pdb=" C TYR A 513 " pdb=" N PHE A 514 " ideal model delta sigma weight residual 118.59 124.93 -6.34 1.63e+00 3.76e-01 1.51e+01 angle pdb=" CA LYS B 125 " pdb=" C LYS B 125 " pdb=" O LYS B 125 " ideal model delta sigma weight residual 122.14 117.37 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 113.00 108.32 4.68 1.30e+00 5.92e-01 1.29e+01 angle pdb=" C2' GTP B 201 " pdb=" C3' GTP B 201 " pdb=" C4' GTP B 201 " ideal model delta sigma weight residual 111.00 100.32 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" O1B GTP B 201 " pdb=" PB GTP B 201 " pdb=" O2B GTP B 201 " ideal model delta sigma weight residual 109.50 119.93 -10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 12014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5303 35.90 - 71.81: 75 71.81 - 107.71: 12 107.71 - 143.61: 1 143.61 - 179.51: 1 Dihedral angle restraints: 5392 sinusoidal: 2169 harmonic: 3223 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -75.89 -179.51 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual -68.92 64.23 -133.15 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O3A GTP B 201 " pdb=" O3B GTP B 201 " pdb=" PB GTP B 201 " pdb=" PG GTP B 201 " ideal model delta sinusoidal sigma weight residual -56.21 -160.47 104.26 1 2.00e+01 2.50e-03 2.99e+01 ... (remaining 5389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1101 0.045 - 0.089: 265 0.089 - 0.134: 55 0.134 - 0.179: 6 0.179 - 0.223: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C3' GTP B 201 " pdb=" C2' GTP B 201 " pdb=" C4' GTP B 201 " pdb=" O3' GTP B 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TYR A 254 " pdb=" N TYR A 254 " pdb=" C TYR A 254 " pdb=" CB TYR A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1425 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 123 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 124 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 563 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 564 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 564 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 564 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 817 " 0.007 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 817 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 817 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 817 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 817 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 817 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 817 " -0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 6738 3.10 - 3.70: 13229 3.70 - 4.30: 19334 4.30 - 4.90: 31592 Nonbonded interactions: 70931 Sorted by model distance: nonbonded pdb=" O3B GTP B 201 " pdb="MG MG B 202 " model vdw 1.897 2.170 nonbonded pdb=" PG GTP B 201 " pdb="MG MG B 202 " model vdw 1.990 2.530 nonbonded pdb=" O2G GTP B 201 " pdb="MG MG B 202 " model vdw 2.015 2.170 nonbonded pdb=" O3G GTP B 201 " pdb="MG MG B 202 " model vdw 2.190 2.170 nonbonded pdb=" OH TYR A 154 " pdb=" OG1 THR A 172 " model vdw 2.225 2.440 ... (remaining 70926 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.280 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.550 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8867 Z= 0.187 Angle : 0.667 10.680 12019 Z= 0.339 Chirality : 0.040 0.223 1428 Planarity : 0.004 0.047 1513 Dihedral : 14.178 179.514 3282 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.26), residues: 1077 helix: 1.02 (0.19), residues: 768 sheet: -0.83 (0.72), residues: 50 loop : 0.49 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.007 0.001 HIS B 32 PHE 0.025 0.002 PHE A 817 TYR 0.019 0.001 TYR A 511 ARG 0.005 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7807 (m-80) cc_final: 0.7531 (m-10) REVERT: A 263 ASP cc_start: 0.7757 (m-30) cc_final: 0.7479 (m-30) REVERT: A 280 MET cc_start: 0.8411 (mmm) cc_final: 0.8199 (mmp) REVERT: A 427 THR cc_start: 0.8201 (p) cc_final: 0.7928 (t) REVERT: A 431 ILE cc_start: 0.7552 (mt) cc_final: 0.7179 (tt) REVERT: A 478 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7740 (ttmm) REVERT: A 578 PHE cc_start: 0.7980 (t80) cc_final: 0.7740 (t80) REVERT: A 611 MET cc_start: 0.7673 (mtp) cc_final: 0.7440 (mtp) REVERT: A 615 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7458 (ttpp) REVERT: A 786 ASN cc_start: 0.8488 (t0) cc_final: 0.8061 (t0) REVERT: A 887 PHE cc_start: 0.8898 (m-10) cc_final: 0.8457 (m-80) REVERT: A 959 MET cc_start: 0.6477 (mmm) cc_final: 0.6276 (mmm) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2375 time to fit residues: 49.2386 Evaluate side-chains 89 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.0030 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 140 HIS ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 627 ASN B 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8867 Z= 0.162 Angle : 0.530 8.321 12019 Z= 0.273 Chirality : 0.039 0.256 1428 Planarity : 0.004 0.043 1513 Dihedral : 8.857 167.967 1161 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.60 % Allowed : 6.04 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.70 (0.26), residues: 1077 helix: 1.59 (0.19), residues: 768 sheet: -1.18 (0.75), residues: 45 loop : 0.39 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 66 HIS 0.004 0.001 HIS B 32 PHE 0.019 0.002 PHE B 28 TYR 0.015 0.001 TYR B 81 ARG 0.005 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7674 (m-30) cc_final: 0.7427 (m-30) REVERT: A 478 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7719 (ttmm) REVERT: A 615 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7226 (ttpp) REVERT: A 887 PHE cc_start: 0.8825 (m-10) cc_final: 0.8524 (m-80) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.2346 time to fit residues: 35.4703 Evaluate side-chains 93 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8867 Z= 0.272 Angle : 0.573 13.262 12019 Z= 0.288 Chirality : 0.041 0.164 1428 Planarity : 0.004 0.037 1513 Dihedral : 8.094 161.192 1161 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.41 % Allowed : 7.34 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.63 (0.26), residues: 1077 helix: 1.63 (0.19), residues: 766 sheet: -1.29 (0.74), residues: 45 loop : 0.07 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.004 0.001 HIS A 308 PHE 0.024 0.002 PHE B 28 TYR 0.017 0.002 TYR A 68 ARG 0.007 0.001 ARG A 825 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7800 (ttmm) REVERT: B 38 GLU cc_start: 0.7614 (tp30) cc_final: 0.7251 (tm-30) REVERT: B 64 ASP cc_start: 0.7774 (t0) cc_final: 0.7489 (t0) REVERT: B 72 GLU cc_start: 0.8075 (tp30) cc_final: 0.7821 (tp30) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.2292 time to fit residues: 30.5554 Evaluate side-chains 92 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8867 Z= 0.165 Angle : 0.493 10.897 12019 Z= 0.249 Chirality : 0.037 0.145 1428 Planarity : 0.003 0.038 1513 Dihedral : 7.563 153.811 1161 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.01 % Allowed : 9.56 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.79 (0.26), residues: 1077 helix: 1.77 (0.19), residues: 765 sheet: -1.21 (0.72), residues: 45 loop : 0.04 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE B 28 TYR 0.018 0.001 TYR A 68 ARG 0.005 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7753 (m-30) cc_final: 0.7303 (m-30) REVERT: A 478 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7742 (ttmm) REVERT: A 574 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 38 GLU cc_start: 0.7666 (tp30) cc_final: 0.7279 (tm-30) REVERT: B 72 GLU cc_start: 0.8129 (tp30) cc_final: 0.7847 (tp30) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.2312 time to fit residues: 31.0006 Evaluate side-chains 89 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8867 Z= 0.167 Angle : 0.489 9.956 12019 Z= 0.248 Chirality : 0.038 0.146 1428 Planarity : 0.003 0.036 1513 Dihedral : 7.287 150.969 1161 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.31 % Allowed : 9.76 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.90 (0.26), residues: 1077 helix: 1.86 (0.19), residues: 763 sheet: -0.54 (0.89), residues: 32 loop : -0.09 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS B 32 PHE 0.016 0.001 PHE B 28 TYR 0.011 0.001 TYR A 697 ARG 0.002 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7686 (m-30) cc_final: 0.7332 (m-30) REVERT: A 478 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7721 (ttmm) REVERT: A 574 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 763 ARG cc_start: 0.7600 (tpt-90) cc_final: 0.7224 (tpt170) REVERT: B 64 ASP cc_start: 0.7712 (t0) cc_final: 0.7465 (t0) REVERT: B 173 ASN cc_start: 0.7355 (t0) cc_final: 0.7030 (p0) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.2230 time to fit residues: 30.2867 Evaluate side-chains 93 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8867 Z= 0.256 Angle : 0.530 9.043 12019 Z= 0.268 Chirality : 0.040 0.165 1428 Planarity : 0.003 0.030 1513 Dihedral : 7.234 149.420 1161 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.61 % Allowed : 10.36 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.80 (0.26), residues: 1077 helix: 1.80 (0.19), residues: 763 sheet: -0.47 (0.92), residues: 32 loop : -0.20 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.003 0.001 HIS A 308 PHE 0.024 0.002 PHE A 745 TYR 0.013 0.001 TYR B 100 ARG 0.006 0.001 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7852 (m-30) cc_final: 0.7319 (m-30) REVERT: A 478 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7788 (ttmm) REVERT: A 574 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8088 (tt) REVERT: A 702 THR cc_start: 0.8247 (t) cc_final: 0.7792 (t) REVERT: A 825 ARG cc_start: 0.8333 (mmt90) cc_final: 0.8030 (tpp-160) REVERT: B 64 ASP cc_start: 0.7805 (t0) cc_final: 0.7540 (t0) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.2162 time to fit residues: 29.1934 Evaluate side-chains 96 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8867 Z= 0.151 Angle : 0.489 9.307 12019 Z= 0.246 Chirality : 0.037 0.178 1428 Planarity : 0.003 0.029 1513 Dihedral : 6.975 145.466 1161 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 11.37 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.99 (0.26), residues: 1077 helix: 1.96 (0.19), residues: 762 sheet: -0.05 (0.83), residues: 39 loop : -0.21 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 127 HIS 0.002 0.000 HIS B 32 PHE 0.019 0.001 PHE A 745 TYR 0.009 0.001 TYR A 511 ARG 0.008 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7609 (mp0) cc_final: 0.6716 (pm20) REVERT: A 284 ASP cc_start: 0.7718 (m-30) cc_final: 0.7278 (m-30) REVERT: A 478 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7728 (ttmm) REVERT: A 574 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7997 (tt) REVERT: A 702 THR cc_start: 0.8117 (t) cc_final: 0.7678 (t) REVERT: A 825 ARG cc_start: 0.8313 (mmt90) cc_final: 0.7978 (tpp-160) REVERT: B 173 ASN cc_start: 0.7364 (t0) cc_final: 0.7118 (p0) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.2227 time to fit residues: 29.0892 Evaluate side-chains 90 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.0170 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8867 Z= 0.222 Angle : 0.530 10.964 12019 Z= 0.264 Chirality : 0.039 0.156 1428 Planarity : 0.003 0.031 1513 Dihedral : 6.972 144.524 1161 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.51 % Allowed : 11.57 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.94 (0.26), residues: 1077 helix: 1.91 (0.19), residues: 764 sheet: 0.02 (0.84), residues: 39 loop : -0.21 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.007 0.001 HIS A 207 PHE 0.021 0.002 PHE A 745 TYR 0.011 0.001 TYR B 100 ARG 0.006 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7919 (m-30) cc_final: 0.7249 (m-30) REVERT: A 478 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7765 (ttmm) REVERT: A 574 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 702 THR cc_start: 0.8104 (t) cc_final: 0.7649 (t) REVERT: A 766 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8133 (mmmt) REVERT: B 64 ASP cc_start: 0.7785 (t0) cc_final: 0.7520 (t0) REVERT: B 173 ASN cc_start: 0.7371 (t0) cc_final: 0.7088 (p0) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.2274 time to fit residues: 30.8518 Evaluate side-chains 95 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8867 Z= 0.166 Angle : 0.512 11.411 12019 Z= 0.254 Chirality : 0.038 0.281 1428 Planarity : 0.003 0.033 1513 Dihedral : 6.815 141.405 1161 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.11 % Allowed : 12.17 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.05 (0.26), residues: 1077 helix: 2.00 (0.19), residues: 763 sheet: 0.07 (0.85), residues: 39 loop : -0.23 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.001 PHE A 745 TYR 0.012 0.001 TYR B 81 ARG 0.008 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7869 (m-30) cc_final: 0.7389 (m-30) REVERT: A 478 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7737 (ttmm) REVERT: A 574 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8032 (tt) REVERT: A 702 THR cc_start: 0.8054 (t) cc_final: 0.7600 (t) REVERT: B 173 ASN cc_start: 0.7354 (t0) cc_final: 0.7080 (p0) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.2427 time to fit residues: 30.9275 Evaluate side-chains 91 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8867 Z= 0.200 Angle : 0.534 12.341 12019 Z= 0.263 Chirality : 0.039 0.257 1428 Planarity : 0.003 0.035 1513 Dihedral : 6.777 139.885 1161 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.31 % Allowed : 11.57 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.04 (0.26), residues: 1077 helix: 2.00 (0.19), residues: 763 sheet: 0.11 (0.86), residues: 39 loop : -0.27 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.002 0.001 HIS B 141 PHE 0.021 0.001 PHE A 745 TYR 0.010 0.001 TYR B 100 ARG 0.009 0.001 ARG A 705 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7926 (m-30) cc_final: 0.7234 (m-30) REVERT: A 478 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7760 (ttmm) REVERT: A 570 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7294 (mtm180) REVERT: A 574 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 702 THR cc_start: 0.8068 (t) cc_final: 0.7626 (t) REVERT: B 64 ASP cc_start: 0.7741 (t0) cc_final: 0.7494 (t0) REVERT: B 128 VAL cc_start: 0.7799 (t) cc_final: 0.7528 (m) REVERT: B 173 ASN cc_start: 0.7354 (t0) cc_final: 0.7073 (p0) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.2190 time to fit residues: 28.6505 Evaluate side-chains 96 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 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 = 0.3855 r_free = 0.3855 target = 0.157146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110039 restraints weight = 11428.971| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.75 r_work: 0.3088 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8867 Z= 0.274 Angle : 0.576 12.097 12019 Z= 0.283 Chirality : 0.041 0.301 1428 Planarity : 0.004 0.035 1513 Dihedral : 6.887 140.124 1161 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.51 % Allowed : 11.47 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.26), residues: 1077 helix: 1.90 (0.19), residues: 762 sheet: 0.02 (0.85), residues: 39 loop : -0.32 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.004 0.001 HIS A 207 PHE 0.021 0.002 PHE A 745 TYR 0.013 0.001 TYR B 100 ARG 0.010 0.001 ARG A 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.02 seconds wall clock time: 35 minutes 50.92 seconds (2150.92 seconds total)