Starting phenix.real_space_refine on Fri Dec 8 07:37:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/12_2023/8sgj_40457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/12_2023/8sgj_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_40457/12_2023/8sgj_40457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/12_2023/8sgj_40457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/12_2023/8sgj_40457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/12_2023/8sgj_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-1.21rc1-5172/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: 4.44, per 1000 atoms: 0.58 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 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: 0.87 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: 2.75 Time building geometry restraints manager: 2.91 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.010 Extract box with map and model: 9.880 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.360 Find NCS groups from input model: 0.200 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- 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 : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2269 time to fit residues: 47.5036 Evaluate side-chains 112 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2372 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7836 Z= 0.284 Angle : 0.550 7.574 10638 Z= 0.301 Chirality : 0.044 0.148 1215 Planarity : 0.004 0.044 1332 Dihedral : 4.375 17.201 1047 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 7.51 % 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: 0.58 (0.26), residues: 966 helix: 1.12 (0.27), residues: 344 sheet: 0.41 (0.29), residues: 304 loop : -0.29 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 709 HIS 0.005 0.001 HIS A 501 PHE 0.017 0.002 PHE A 925 TYR 0.014 0.002 TYR L 93 ARG 0.007 0.001 ARG A 894 *********************** 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: 13 poor density : 111 time to evaluate : 0.834 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.1915 time to fit residues: 31.7365 Evaluate side-chains 106 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0775 time to fit residues: 2.4800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7836 Z= 0.388 Angle : 0.579 6.912 10638 Z= 0.316 Chirality : 0.045 0.160 1215 Planarity : 0.004 0.041 1332 Dihedral : 4.419 16.810 1047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 11.38 % Favored : 87.77 % 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: 0.49 (0.26), residues: 966 helix: 1.15 (0.26), residues: 348 sheet: 0.22 (0.29), residues: 309 loop : -0.32 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 709 HIS 0.006 0.001 HIS A 501 PHE 0.016 0.002 PHE A 587 TYR 0.019 0.002 TYR A 180 ARG 0.005 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 109 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.1974 time to fit residues: 29.0231 Evaluate side-chains 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0711 time to fit residues: 1.6830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8199 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7836 Z= 0.179 Angle : 0.486 7.642 10638 Z= 0.265 Chirality : 0.041 0.146 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.241 18.163 1047 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.97 % Allowed : 12.23 % Favored : 86.80 % 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: 0.80 (0.27), residues: 966 helix: 1.64 (0.27), residues: 343 sheet: 0.29 (0.29), residues: 309 loop : -0.33 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 709 HIS 0.003 0.001 HIS A 789 PHE 0.013 0.001 PHE A 587 TYR 0.012 0.001 TYR L 93 ARG 0.003 0.000 ARG A 894 *********************** 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 115 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.872 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.1998 time to fit residues: 30.1612 Evaluate side-chains 98 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0675 time to fit residues: 1.5311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 7836 Z= 0.426 Angle : 0.574 9.089 10638 Z= 0.311 Chirality : 0.045 0.161 1215 Planarity : 0.004 0.039 1332 Dihedral : 4.388 18.865 1047 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.85 % Allowed : 13.56 % Favored : 85.59 % 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: 0.50 (0.27), residues: 966 helix: 1.38 (0.27), residues: 348 sheet: 0.09 (0.30), residues: 293 loop : -0.45 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 709 HIS 0.006 0.001 HIS A 789 PHE 0.017 0.002 PHE A 587 TYR 0.018 0.002 TYR A 180 ARG 0.003 0.001 ARG H 59 *********************** 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 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.833 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 103 average time/residue: 0.1894 time to fit residues: 27.1945 Evaluate side-chains 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0747 time to fit residues: 1.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7836 Z= 0.275 Angle : 0.520 8.966 10638 Z= 0.281 Chirality : 0.042 0.145 1215 Planarity : 0.004 0.037 1332 Dihedral : 4.334 18.554 1047 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.36 % Allowed : 15.01 % Favored : 84.62 % 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: 0.54 (0.27), residues: 966 helix: 1.52 (0.27), residues: 344 sheet: 0.04 (0.30), residues: 304 loop : -0.45 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 709 HIS 0.004 0.001 HIS A 789 PHE 0.015 0.001 PHE A 587 TYR 0.014 0.002 TYR A 180 ARG 0.003 0.000 ARG A 894 *********************** 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 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.915 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.1890 time to fit residues: 26.8996 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0687 time to fit residues: 1.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.0370 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6462 ------------------------------------------------------------------------------- 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 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7836 Z= 0.173 Angle : 0.486 10.797 10638 Z= 0.260 Chirality : 0.041 0.147 1215 Planarity : 0.003 0.034 1332 Dihedral : 4.139 18.354 1047 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.61 % Allowed : 15.86 % 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: 0.87 (0.27), residues: 966 helix: 1.85 (0.27), residues: 343 sheet: 0.18 (0.30), residues: 314 loop : -0.31 (0.36), residues: 309 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 0.013 0.001 PHE A 587 TYR 0.010 0.001 TYR A 180 ARG 0.003 0.000 ARG H 13 *********************** 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 102 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.653 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.1556 time to fit residues: 21.6237 Evaluate side-chains 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0734 time to fit residues: 1.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7836 Z= 0.295 Angle : 0.534 10.913 10638 Z= 0.285 Chirality : 0.043 0.163 1215 Planarity : 0.004 0.037 1332 Dihedral : 4.229 18.121 1047 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.24 % Allowed : 16.46 % Favored : 83.29 % 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: 0.78 (0.27), residues: 966 helix: 1.70 (0.27), residues: 346 sheet: 0.07 (0.30), residues: 298 loop : -0.20 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 709 HIS 0.004 0.001 HIS A 789 PHE 0.016 0.002 PHE A 587 TYR 0.016 0.002 TYR A 180 ARG 0.003 0.000 ARG H 98 *********************** 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 102 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.872 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2088 time to fit residues: 28.6498 Evaluate side-chains 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0781 time to fit residues: 1.3081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7836 Z= 0.153 Angle : 0.484 11.766 10638 Z= 0.259 Chirality : 0.041 0.154 1215 Planarity : 0.003 0.035 1332 Dihedral : 4.088 17.361 1047 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.61 % Allowed : 16.46 % Favored : 82.93 % 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: 1.00 (0.27), residues: 966 helix: 2.01 (0.27), residues: 339 sheet: 0.15 (0.30), residues: 297 loop : -0.13 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 709 HIS 0.003 0.001 HIS A 789 PHE 0.012 0.001 PHE A 587 TYR 0.010 0.001 TYR A 180 ARG 0.005 0.000 ARG A 661 *********************** 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 105 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.830 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 103 average time/residue: 0.2228 time to fit residues: 32.1258 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0762 time to fit residues: 1.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7836 Z= 0.174 Angle : 0.490 11.789 10638 Z= 0.260 Chirality : 0.041 0.160 1215 Planarity : 0.003 0.034 1332 Dihedral : 4.046 16.997 1047 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 16.71 % Favored : 83.29 % 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: 1.05 (0.27), residues: 966 helix: 2.01 (0.27), residues: 343 sheet: 0.15 (0.30), residues: 297 loop : -0.06 (0.35), residues: 326 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 0.019 0.001 PHE A 925 TYR 0.015 0.001 TYR A 892 ARG 0.002 0.000 ARG A 547 ********************** 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 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.873 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1893 time to fit residues: 25.2264 Evaluate side-chains 94 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096119 restraints weight = 10123.073| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.87 r_work: 0.3002 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3438 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= 0.288 Angle : 0.539 11.860 10638 Z= 0.287 Chirality : 0.043 0.150 1215 Planarity : 0.004 0.038 1332 Dihedral : 4.179 17.845 1047 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 0.61 % Allowed : 16.83 % Favored : 82.57 % 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: 0.84 (0.27), residues: 966 helix: 1.77 (0.27), residues: 345 sheet: 0.02 (0.30), residues: 298 loop : -0.09 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 709 HIS 0.004 0.001 HIS A 789 PHE 0.015 0.002 PHE A 587 TYR 0.017 0.002 TYR A 180 ARG 0.003 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.28 seconds wall clock time: 36 minutes 21.60 seconds (2181.60 seconds total)