Starting phenix.real_space_refine on Fri Dec 8 08:27:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/12_2023/7rqs_24635.pdb" } resolution = 3.57 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= 0.002 sd= 0.028 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 48 5.16 5 C 4898 2.51 5 N 1349 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7792 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 7792 Unusual residues: {' MG': 1} Classifications: {'peptide': 1074, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 38, 'TRANS': 1035, None: 1} Not linked: pdbres="GLN A1121 " pdbres=" MG A1201 " Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1087 Unresolved non-hydrogen dihedrals: 768 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 20, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 15, 'GLU:plan': 21, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 522 Time building chain proxies: 4.90, per 1000 atoms: 0.63 Number of scatterers: 7792 At special positions: 0 Unit cell: (81.024, 101.28, 108.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 Mg 1 11.99 O 1496 8.00 N 1349 7.00 C 4898 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: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 38.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.546A pdb=" N LEU A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.657A pdb=" N SER A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.596A pdb=" N THR A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 295 through 305 removed outlier: 4.155A pdb=" N ALA A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 315 through 325 removed outlier: 3.704A pdb=" N MET A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 5.610A pdb=" N SER A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.531A pdb=" N LEU A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 4.438A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 645 through 662 removed outlier: 3.981A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 650 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.872A pdb=" N ALA A 669 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 671 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 Processing helix chain 'A' and resid 699 through 720 Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.517A pdb=" N CYS A 826 " --> pdb=" O HIS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.611A pdb=" N ILE A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 921 Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.864A pdb=" N ARG A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 991 removed outlier: 3.812A pdb=" N GLU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1018 removed outlier: 4.259A pdb=" N ALA A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A1008 " --> pdb=" O ASP A1004 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1068 removed outlier: 3.563A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.030A pdb=" N VAL A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.604A pdb=" N GLN A 60 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 4.018A pdb=" N MET A 218 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 195 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 220 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 155 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 142 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 127 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 113 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE A 109 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A 133 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A 107 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP A 135 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 105 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 110 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N LEU A 262 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 168 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 125 removed outlier: 3.653A pdb=" N ALA A 125 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 400 removed outlier: 5.527A pdb=" N LEU A 393 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 385 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 395 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 383 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE A 415 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 382 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 417 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TRP A 485 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.655A pdb=" N LEU A 618 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 560 removed outlier: 6.371A pdb=" N GLY A 558 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 622 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.384A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 812 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 732 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 814 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS A 734 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 811 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG A 749 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 748 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.384A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 748 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.396A pdb=" N PHE A 939 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 323 hydrogen bonds defined for protein. 924 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: 4.42 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2101 1.33 - 1.45: 1219 1.45 - 1.57: 4516 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 7910 Sorted by residual: bond pdb=" C ARG A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.332 1.367 -0.035 1.32e-02 5.74e+03 7.05e+00 bond pdb=" N VAL A 100 " pdb=" CA VAL A 100 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N ARG A 98 " pdb=" CA ARG A 98 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.70e-02 3.46e+03 5.23e+00 bond pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.33e-02 5.65e+03 4.77e+00 bond pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.76e-02 3.23e+03 3.00e+00 ... (remaining 7905 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.90: 149 105.90 - 112.91: 4365 112.91 - 119.93: 2525 119.93 - 126.95: 3628 126.95 - 133.96: 68 Bond angle restraints: 10735 Sorted by residual: angle pdb=" N PRO A 99 " pdb=" CA PRO A 99 " pdb=" CB PRO A 99 " ideal model delta sigma weight residual 103.34 106.68 -3.34 9.30e-01 1.16e+00 1.29e+01 angle pdb=" CA VAL A 100 " pdb=" C VAL A 100 " pdb=" O VAL A 100 " ideal model delta sigma weight residual 120.95 117.68 3.27 1.04e+00 9.25e-01 9.86e+00 angle pdb=" N GLN A 570 " pdb=" CA GLN A 570 " pdb=" CB GLN A 570 " ideal model delta sigma weight residual 110.16 114.68 -4.52 1.48e+00 4.57e-01 9.34e+00 angle pdb=" N PRO A 97 " pdb=" CA PRO A 97 " pdb=" C PRO A 97 " ideal model delta sigma weight residual 112.47 118.50 -6.03 2.06e+00 2.36e-01 8.57e+00 angle pdb=" CA ILE A 96 " pdb=" C ILE A 96 " pdb=" N PRO A 97 " ideal model delta sigma weight residual 119.42 122.14 -2.72 9.30e-01 1.16e+00 8.55e+00 ... (remaining 10730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4328 17.20 - 34.40: 377 34.40 - 51.59: 80 51.59 - 68.79: 9 68.79 - 85.99: 3 Dihedral angle restraints: 4797 sinusoidal: 1675 harmonic: 3122 Sorted by residual: dihedral pdb=" CA GLU A 117 " pdb=" C GLU A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 174 " pdb=" CB ASP A 174 " pdb=" CG ASP A 174 " pdb=" OD1 ASP A 174 " ideal model delta sinusoidal sigma weight residual -30.00 -82.65 52.65 1 2.00e+01 2.50e-03 9.44e+00 dihedral pdb=" N VAL A 100 " pdb=" CA VAL A 100 " pdb=" CB VAL A 100 " pdb=" CG1 VAL A 100 " ideal model delta sinusoidal sigma weight residual 60.00 8.22 51.78 3 1.50e+01 4.44e-03 9.05e+00 ... (remaining 4794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 928 0.040 - 0.080: 247 0.080 - 0.120: 89 0.120 - 0.161: 6 0.161 - 0.201: 3 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" C PRO A 97 " pdb=" CB PRO A 97 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR A 463 " pdb=" CA THR A 463 " pdb=" OG1 THR A 463 " pdb=" CG2 THR A 463 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB VAL A 100 " pdb=" CA VAL A 100 " pdb=" CG1 VAL A 100 " pdb=" CG2 VAL A 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 1270 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 845 " 0.066 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 846 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 846 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 846 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 850 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO A 851 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 346 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 347 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.022 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 90 2.65 - 3.21: 7505 3.21 - 3.78: 11846 3.78 - 4.34: 15587 4.34 - 4.90: 25512 Nonbonded interactions: 60540 Sorted by model distance: nonbonded pdb=" OD1 ASP A 832 " pdb="MG MG A1201 " model vdw 2.088 2.170 nonbonded pdb=" O SER A 682 " pdb=" NZ LYS A 688 " model vdw 2.213 2.520 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.255 2.440 nonbonded pdb=" NH2 ARG A 506 " pdb=" O ASP A 612 " model vdw 2.257 2.520 nonbonded pdb=" O GLY A 503 " pdb=" NH1 ARG A 506 " model vdw 2.267 2.520 ... (remaining 60535 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: 31.300 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: 0.000 Extract box with map and model: 26.270 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 0.039 7910 Z= 0.172 Angle : 0.544 7.784 10735 Z= 0.301 Chirality : 0.041 0.201 1273 Planarity : 0.004 0.099 1400 Dihedral : 13.383 85.988 2757 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % 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: -0.91 (0.26), residues: 1057 helix: 1.27 (0.29), residues: 354 sheet: -1.41 (0.44), residues: 142 loop : -1.67 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.002 0.001 HIS A 710 PHE 0.010 0.001 PHE A 471 TYR 0.023 0.001 TYR A 799 ARG 0.007 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.811 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.2163 time to fit residues: 45.7001 Evaluate side-chains 136 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0685 time to fit residues: 1.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 7910 Z= 0.438 Angle : 0.682 9.123 10735 Z= 0.362 Chirality : 0.047 0.190 1273 Planarity : 0.005 0.059 1400 Dihedral : 4.895 19.792 1124 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.85 % Allowed : 11.21 % Favored : 86.94 % 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: -1.51 (0.25), residues: 1057 helix: 0.27 (0.27), residues: 373 sheet: -1.35 (0.44), residues: 144 loop : -1.85 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 485 HIS 0.009 0.002 HIS A 411 PHE 0.025 0.002 PHE A 471 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.940 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 157 average time/residue: 0.2043 time to fit residues: 44.0620 Evaluate side-chains 156 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0815 time to fit residues: 2.1270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 86 optimal weight: 0.0970 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 overall best weight: 0.1430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS A 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7910 Z= 0.130 Angle : 0.504 9.420 10735 Z= 0.263 Chirality : 0.041 0.172 1273 Planarity : 0.004 0.054 1400 Dihedral : 4.040 16.959 1124 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 0.92 % Allowed : 16.75 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1057 helix: 0.82 (0.28), residues: 371 sheet: -1.18 (0.44), residues: 140 loop : -1.61 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 129 HIS 0.005 0.001 HIS A 411 PHE 0.031 0.001 PHE A 957 TYR 0.020 0.001 TYR A 879 ARG 0.003 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 155 average time/residue: 0.2006 time to fit residues: 43.0285 Evaluate side-chains 148 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2099 time to fit residues: 1.8530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7910 Z= 0.461 Angle : 0.659 8.384 10735 Z= 0.356 Chirality : 0.047 0.174 1273 Planarity : 0.005 0.049 1400 Dihedral : 4.874 20.594 1124 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 2.64 % Allowed : 18.73 % Favored : 78.63 % 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: -1.50 (0.25), residues: 1057 helix: 0.30 (0.27), residues: 371 sheet: -1.35 (0.43), residues: 150 loop : -1.86 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 485 HIS 0.011 0.002 HIS A 411 PHE 0.028 0.002 PHE A 471 TYR 0.026 0.002 TYR A 879 ARG 0.004 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.888 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 162 average time/residue: 0.1957 time to fit residues: 44.2217 Evaluate side-chains 164 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0730 time to fit residues: 3.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7910 Z= 0.207 Angle : 0.553 10.648 10735 Z= 0.291 Chirality : 0.042 0.160 1273 Planarity : 0.004 0.047 1400 Dihedral : 4.382 19.849 1124 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 1.45 % Allowed : 20.32 % Favored : 78.23 % 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: -1.29 (0.26), residues: 1057 helix: 0.58 (0.28), residues: 372 sheet: -1.36 (0.43), residues: 145 loop : -1.77 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.027 0.001 PHE A 957 TYR 0.025 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 0.828 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 160 average time/residue: 0.1974 time to fit residues: 43.4537 Evaluate side-chains 151 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0790 time to fit residues: 2.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7910 Z= 0.231 Angle : 0.584 13.035 10735 Z= 0.302 Chirality : 0.043 0.166 1273 Planarity : 0.004 0.046 1400 Dihedral : 4.403 19.687 1124 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.46 % Favored : 90.44 % Rotamer: Outliers : 0.92 % Allowed : 22.69 % Favored : 76.39 % 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: -1.27 (0.26), residues: 1057 helix: 0.61 (0.28), residues: 370 sheet: -1.38 (0.43), residues: 145 loop : -1.76 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.025 0.002 PHE A 957 TYR 0.021 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.786 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 150 average time/residue: 0.1928 time to fit residues: 39.9925 Evaluate side-chains 151 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1789 time to fit residues: 2.6390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7910 Z= 0.248 Angle : 0.596 13.159 10735 Z= 0.308 Chirality : 0.043 0.159 1273 Planarity : 0.004 0.048 1400 Dihedral : 4.447 18.821 1124 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.99 % Favored : 90.92 % Rotamer: Outliers : 1.06 % Allowed : 22.56 % Favored : 76.39 % 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 (0.26), residues: 1057 helix: 0.61 (0.28), residues: 369 sheet: -1.37 (0.43), residues: 145 loop : -1.76 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.008 0.001 HIS A 411 PHE 0.028 0.002 PHE A 957 TYR 0.022 0.001 TYR A 879 ARG 0.002 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 155 average time/residue: 0.1979 time to fit residues: 42.6277 Evaluate side-chains 155 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0854 time to fit residues: 2.0211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.0570 chunk 93 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7910 Z= 0.166 Angle : 0.553 12.003 10735 Z= 0.284 Chirality : 0.041 0.152 1273 Planarity : 0.004 0.049 1400 Dihedral : 4.158 17.951 1124 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.70 % Favored : 91.20 % Rotamer: Outliers : 0.40 % Allowed : 23.75 % Favored : 75.86 % 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: -1.07 (0.26), residues: 1057 helix: 0.87 (0.28), residues: 366 sheet: -1.31 (0.43), residues: 147 loop : -1.69 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.029 0.001 PHE A 957 TYR 0.020 0.001 TYR A 879 ARG 0.002 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 0.858 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.1987 time to fit residues: 41.0146 Evaluate side-chains 149 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0779 time to fit residues: 1.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.0070 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 478 GLN A 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7910 Z= 0.144 Angle : 0.538 11.258 10735 Z= 0.277 Chirality : 0.041 0.158 1273 Planarity : 0.004 0.049 1400 Dihedral : 3.959 19.669 1124 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 0.40 % Allowed : 24.67 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.26), residues: 1057 helix: 1.06 (0.28), residues: 371 sheet: -1.11 (0.44), residues: 142 loop : -1.62 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.031 0.001 PHE A 957 TYR 0.018 0.001 TYR A 879 ARG 0.003 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 0.984 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 149 average time/residue: 0.2088 time to fit residues: 42.6922 Evaluate side-chains 146 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0733 time to fit residues: 1.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 0.0020 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7910 Z= 0.253 Angle : 0.606 11.680 10735 Z= 0.314 Chirality : 0.043 0.168 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.298 19.037 1124 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.18 % Favored : 90.73 % Rotamer: Outliers : 0.26 % Allowed : 24.67 % Favored : 75.07 % 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: -1.04 (0.26), residues: 1057 helix: 0.93 (0.28), residues: 369 sheet: -1.27 (0.43), residues: 147 loop : -1.72 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.010 0.001 HIS A 411 PHE 0.028 0.002 PHE A 957 TYR 0.026 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 0.865 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.1989 time to fit residues: 40.7759 Evaluate side-chains 146 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150384 restraints weight = 10795.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154425 restraints weight = 6019.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157135 restraints weight = 4010.895| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7910 Z= 0.221 Angle : 0.603 11.705 10735 Z= 0.307 Chirality : 0.043 0.174 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.250 19.313 1124 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.89 % Favored : 91.01 % Rotamer: Outliers : 0.40 % Allowed : 24.80 % Favored : 74.80 % 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: -1.05 (0.26), residues: 1057 helix: 0.90 (0.28), residues: 368 sheet: -1.26 (0.43), residues: 147 loop : -1.71 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.028 0.002 PHE A 957 TYR 0.024 0.001 TYR A 879 ARG 0.002 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.22 seconds wall clock time: 51 minutes 7.81 seconds (3067.81 seconds total)