Starting phenix.real_space_refine on Sat Apr 6 08:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/04_2024/8sgj_40457.pdb" } resolution = 3.1 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 31 5.16 5 Na 3 4.78 5 C 4948 2.51 5 N 1242 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7667 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5900 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 6, ' NA': 3} Classifications: {'undetermined': 9, 'water': 1} Link IDs: {None: 9} Time building chain proxies: 4.40, per 1000 atoms: 0.57 Number of scatterers: 7667 At special positions: 0 Unit cell: (97.11, 100.43, 146.08, 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) Ca 6 19.99 S 31 16.00 Na 3 11.00 O 1437 8.00 N 1242 7.00 C 4948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 36 through 72 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.517A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.511A pdb=" N HIS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 155 removed outlier: 3.821A pdb=" N ILE A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.784A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 4.507A pdb=" N PHE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.593A pdb=" N VAL A 227 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.597A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 755 removed outlier: 5.420A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.725A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.742A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 788 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 removed outlier: 3.714A pdb=" N ASP A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.583A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.996A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.592A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.780A pdb=" N TYR A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.816A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.582A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.614A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79 removed outlier: 4.365A pdb=" N TYR A 228 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.262A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 443 Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.894A pdb=" N TYR A 381 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 497 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL A 458 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 412 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU A 460 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 410 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN A 462 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 408 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 574 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.842A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.842A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 534 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL A 597 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 627 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 616 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.546A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.546A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.466A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1182 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: 2.92 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2308 1.34 - 1.46: 1441 1.46 - 1.57: 4042 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7836 Sorted by residual: bond pdb=" CB TRP A 29 " pdb=" CG TRP A 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.33e+00 bond pdb=" CA TYR H 60 " pdb=" C TYR H 60 " ideal model delta sigma weight residual 1.521 1.496 0.025 1.23e-02 6.61e+03 4.16e+00 bond pdb=" N TRP A 29 " pdb=" CA TRP A 29 " ideal model delta sigma weight residual 1.455 1.434 0.021 1.30e-02 5.92e+03 2.69e+00 bond pdb=" CA LYS A 697 " pdb=" CB LYS A 697 " ideal model delta sigma weight residual 1.527 1.567 -0.039 2.48e-02 1.63e+03 2.52e+00 bond pdb=" C TYR H 60 " pdb=" O TYR H 60 " ideal model delta sigma weight residual 1.234 1.218 0.016 1.22e-02 6.72e+03 1.68e+00 ... (remaining 7831 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.21: 158 106.21 - 113.20: 4231 113.20 - 120.19: 2849 120.19 - 127.17: 3313 127.17 - 134.16: 87 Bond angle restraints: 10638 Sorted by residual: angle pdb=" N TRP A 29 " pdb=" CA TRP A 29 " pdb=" C TRP A 29 " ideal model delta sigma weight residual 110.20 103.08 7.12 1.58e+00 4.01e-01 2.03e+01 angle pdb=" N GLN H 82 " pdb=" CA GLN H 82 " pdb=" C GLN H 82 " ideal model delta sigma weight residual 109.07 115.29 -6.22 1.61e+00 3.86e-01 1.49e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C TYR H 60 " pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " ideal model delta sigma weight residual 110.45 102.87 7.58 2.15e+00 2.16e-01 1.24e+01 angle pdb=" C ILE A 643 " pdb=" N ALA A 644 " pdb=" CA ALA A 644 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 ... (remaining 10633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4166 17.09 - 34.19: 320 34.19 - 51.28: 55 51.28 - 68.37: 5 68.37 - 85.47: 8 Dihedral angle restraints: 4554 sinusoidal: 1746 harmonic: 2808 Sorted by residual: dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" C TYR H 60 " pdb=" N TYR H 60 " pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " ideal model delta harmonic sigma weight residual -122.60 -113.98 -8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" CA GLY A 549 " pdb=" C GLY A 549 " pdb=" N GLY A 550 " pdb=" CA GLY A 550 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 860 0.046 - 0.093: 271 0.093 - 0.139: 75 0.139 - 0.186: 6 0.186 - 0.232: 3 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CB THR A 642 " pdb=" CA THR A 642 " pdb=" OG1 THR A 642 " pdb=" CG2 THR A 642 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 717 " pdb=" CA ILE A 717 " pdb=" CG1 ILE A 717 " pdb=" CG2 ILE A 717 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB THR A 877 " pdb=" CA THR A 877 " pdb=" OG1 THR A 877 " pdb=" CG2 THR A 877 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1212 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 28 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ILE A 28 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 28 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP A 29 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 133 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 812 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 813 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.027 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 84 2.58 - 3.16: 5975 3.16 - 3.74: 11638 3.74 - 4.32: 16557 4.32 - 4.90: 28278 Nonbonded interactions: 62532 Sorted by model distance: nonbonded pdb=" OE2 GLU A 451 " pdb="CA CA A1003 " model vdw 1.994 2.510 nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1003 " model vdw 2.115 2.510 nonbonded pdb=" OD1 ASP A 421 " pdb="CA CA A1003 " model vdw 2.182 2.510 nonbonded pdb=" OD1 ASP A 408 " pdb=" OG1 THR A 428 " model vdw 2.188 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.204 2.440 ... (remaining 62527 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: 2.270 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: 9.790 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.530 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.004 0.065 7836 Z= 0.263 Angle : 0.699 9.269 10638 Z= 0.385 Chirality : 0.048 0.232 1215 Planarity : 0.006 0.063 1332 Dihedral : 12.734 85.467 2747 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.02 (0.26), residues: 966 helix: -0.03 (0.25), residues: 342 sheet: 0.49 (0.29), residues: 311 loop : -0.24 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 95 HIS 0.003 0.001 HIS A 243 PHE 0.028 0.002 PHE A 925 TYR 0.029 0.002 TYR A 46 ARG 0.009 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8276 (mmm) cc_final: 0.8032 (mmm) REVERT: A 62 ASP cc_start: 0.7920 (t70) cc_final: 0.7643 (t0) REVERT: A 162 LYS cc_start: 0.7887 (tttp) cc_final: 0.7024 (tttp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2197 time to fit residues: 46.2398 Evaluate side-chains 113 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 789 HIS ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7836 Z= 0.287 Angle : 0.553 7.335 10638 Z= 0.302 Chirality : 0.044 0.151 1215 Planarity : 0.004 0.045 1332 Dihedral : 4.375 17.124 1047 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.45 % Allowed : 7.63 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.60 (0.27), residues: 966 helix: 1.15 (0.27), residues: 344 sheet: 0.41 (0.29), residues: 304 loop : -0.30 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 709 HIS 0.005 0.001 HIS A 501 PHE 0.018 0.002 PHE A 925 TYR 0.014 0.002 TYR A 180 ARG 0.005 0.001 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8544 (mmm) cc_final: 0.8183 (mmm) REVERT: A 209 ILE cc_start: 0.8664 (mm) cc_final: 0.8255 (mt) outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 0.1946 time to fit residues: 32.3591 Evaluate side-chains 108 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7836 Z= 0.265 Angle : 0.522 6.843 10638 Z= 0.284 Chirality : 0.043 0.177 1215 Planarity : 0.004 0.039 1332 Dihedral : 4.281 16.643 1047 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 9.69 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 966 helix: 1.46 (0.27), residues: 343 sheet: 0.31 (0.29), residues: 309 loop : -0.29 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 709 HIS 0.004 0.001 HIS A 789 PHE 0.015 0.002 PHE A 587 TYR 0.015 0.002 TYR A 180 ARG 0.003 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8537 (mmm) cc_final: 0.8218 (mmm) REVERT: A 764 ASN cc_start: 0.7213 (t0) cc_final: 0.6988 (t0) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.1730 time to fit residues: 28.1502 Evaluate side-chains 108 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7836 Z= 0.200 Angle : 0.490 10.341 10638 Z= 0.264 Chirality : 0.042 0.143 1215 Planarity : 0.003 0.038 1332 Dihedral : 4.170 17.185 1047 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.94 % Allowed : 11.14 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.27), residues: 966 helix: 1.72 (0.27), residues: 343 sheet: 0.37 (0.29), residues: 309 loop : -0.28 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 709 HIS 0.003 0.001 HIS A 789 PHE 0.014 0.001 PHE A 587 TYR 0.013 0.001 TYR A 180 ARG 0.003 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8472 (mmm) cc_final: 0.8153 (mmm) REVERT: A 94 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8706 (mt) REVERT: A 764 ASN cc_start: 0.7238 (t0) cc_final: 0.6983 (t0) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.1725 time to fit residues: 28.0460 Evaluate side-chains 110 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7836 Z= 0.235 Angle : 0.489 6.974 10638 Z= 0.266 Chirality : 0.042 0.161 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.117 17.283 1047 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.66 % Allowed : 11.50 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.92 (0.27), residues: 966 helix: 1.74 (0.27), residues: 348 sheet: 0.31 (0.30), residues: 309 loop : -0.25 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 709 HIS 0.004 0.001 HIS A 789 PHE 0.015 0.001 PHE A 587 TYR 0.014 0.001 TYR A 180 ARG 0.002 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.852 Fit side-chains REVERT: A 53 MET cc_start: 0.8512 (mmm) cc_final: 0.8177 (mmm) REVERT: A 94 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8716 (mt) REVERT: A 764 ASN cc_start: 0.7392 (t0) cc_final: 0.7189 (t0) REVERT: L 95 ASN cc_start: 0.8322 (p0) cc_final: 0.8100 (p0) REVERT: H 13 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7771 (mmm160) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1790 time to fit residues: 30.0387 Evaluate side-chains 112 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7836 Z= 0.336 Angle : 0.540 10.236 10638 Z= 0.289 Chirality : 0.043 0.158 1215 Planarity : 0.004 0.038 1332 Dihedral : 4.253 17.604 1047 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.42 % Allowed : 12.59 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 966 helix: 1.58 (0.27), residues: 348 sheet: 0.19 (0.30), residues: 314 loop : -0.31 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 709 HIS 0.005 0.001 HIS A 789 PHE 0.015 0.002 PHE A 587 TYR 0.018 0.002 TYR A 180 ARG 0.002 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.837 Fit side-chains REVERT: A 53 MET cc_start: 0.8645 (mmm) cc_final: 0.8269 (mmm) REVERT: A 94 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8728 (mt) REVERT: L 95 ASN cc_start: 0.8357 (p0) cc_final: 0.8153 (p0) REVERT: H 13 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7496 (mmm160) outliers start: 20 outliers final: 18 residues processed: 111 average time/residue: 0.1774 time to fit residues: 28.2197 Evaluate side-chains 112 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.0030 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7836 Z= 0.167 Angle : 0.474 11.030 10638 Z= 0.254 Chirality : 0.041 0.147 1215 Planarity : 0.003 0.034 1332 Dihedral : 4.090 16.811 1047 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.94 % Allowed : 14.41 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 966 helix: 1.94 (0.27), residues: 343 sheet: 0.23 (0.30), residues: 304 loop : -0.24 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.012 0.001 PHE A 587 TYR 0.011 0.001 TYR A 180 ARG 0.003 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.837 Fit side-chains REVERT: A 53 MET cc_start: 0.8498 (mmm) cc_final: 0.8165 (mmm) REVERT: A 94 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8729 (mt) REVERT: L 95 ASN cc_start: 0.8364 (p0) cc_final: 0.8153 (p0) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.1872 time to fit residues: 30.1612 Evaluate side-chains 106 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 46 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 90 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 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 789 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7836 Z= 0.174 Angle : 0.509 13.323 10638 Z= 0.268 Chirality : 0.041 0.144 1215 Planarity : 0.003 0.033 1332 Dihedral : 4.126 25.723 1047 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.18 % Allowed : 14.16 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.27), residues: 966 helix: 2.08 (0.27), residues: 344 sheet: 0.23 (0.30), residues: 303 loop : -0.18 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.017 0.001 PHE A 925 TYR 0.011 0.001 TYR A 180 ARG 0.005 0.000 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8494 (mmm) cc_final: 0.8159 (mmm) REVERT: A 94 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8738 (mt) REVERT: L 95 ASN cc_start: 0.8342 (p0) cc_final: 0.8139 (p0) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.1907 time to fit residues: 28.4822 Evaluate side-chains 109 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7836 Z= 0.238 Angle : 0.521 11.569 10638 Z= 0.275 Chirality : 0.042 0.144 1215 Planarity : 0.003 0.035 1332 Dihedral : 4.174 26.164 1047 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.42 % Allowed : 13.68 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 966 helix: 1.92 (0.27), residues: 349 sheet: 0.20 (0.31), residues: 294 loop : -0.12 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 PHE 0.014 0.001 PHE A 587 TYR 0.014 0.001 TYR A 180 ARG 0.004 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8546 (mmm) cc_final: 0.8177 (mmm) REVERT: A 94 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8752 (mt) outliers start: 20 outliers final: 18 residues processed: 111 average time/residue: 0.1926 time to fit residues: 29.7321 Evaluate side-chains 114 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7836 Z= 0.174 Angle : 0.496 11.923 10638 Z= 0.263 Chirality : 0.041 0.145 1215 Planarity : 0.003 0.035 1332 Dihedral : 4.108 27.131 1047 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.18 % Allowed : 14.29 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.12 (0.27), residues: 966 helix: 2.08 (0.27), residues: 344 sheet: 0.23 (0.30), residues: 293 loop : -0.09 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.031 0.001 PHE A 925 TYR 0.011 0.001 TYR A 180 ARG 0.003 0.000 ARG H 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8512 (mmm) cc_final: 0.8163 (mmm) REVERT: A 94 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8728 (mt) outliers start: 18 outliers final: 17 residues processed: 113 average time/residue: 0.1842 time to fit residues: 29.2898 Evaluate side-chains 115 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099622 restraints weight = 10031.973| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.91 r_work: 0.3049 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.170 Angle : 0.492 12.075 10638 Z= 0.260 Chirality : 0.041 0.143 1215 Planarity : 0.003 0.035 1332 Dihedral : 4.068 25.700 1047 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 14.16 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.17 (0.27), residues: 966 helix: 2.13 (0.27), residues: 344 sheet: 0.24 (0.30), residues: 293 loop : -0.05 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.003 0.001 HIS A 243 PHE 0.013 0.001 PHE A 587 TYR 0.016 0.001 TYR A 892 ARG 0.004 0.000 ARG H 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.59 seconds wall clock time: 35 minutes 13.14 seconds (2113.14 seconds total)