Starting phenix.real_space_refine on Mon Sep 23 21:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/09_2024/8cpe_16780.cif" } resolution = 4.0 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 1795 2.51 5 N 470 2.21 5 O 625 1.98 5 H 2615 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5520 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "B" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "E" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 3.44, per 1000 atoms: 0.62 Number of scatterers: 5520 At special positions: 0 Unit cell: (81.5308, 64.7779, 44.6744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 625 8.00 N 470 7.00 C 1795 6.00 H 2615 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.45 Conformation dependent library (CDL) restraints added in 379.2 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.335A pdb=" N MET A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET C 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET D 3 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.578A pdb=" N VAL A 10 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 10 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.186A pdb=" N THR A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR C 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.423A pdb=" N ALA A 27 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER C 28 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.556A pdb=" N TYR C 33 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 74 removed outlier: 6.172A pdb=" N ILE A 67 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER B 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER A 69 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER A 71 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA B 74 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 73 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 71 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 67 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER D 70 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER C 69 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN D 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER C 71 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA D 74 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER C 73 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 67 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER E 70 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER D 69 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER D 71 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA E 74 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER D 73 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.645A pdb=" N THR C 77 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 99 removed outlier: 3.625A pdb=" N ASP A 85 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 82 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP B 85 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU C 84 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA B 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU C 86 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR B 89 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP C 88 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N CYS B 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR C 90 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N SER B 93 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN C 92 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 95 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 94 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASN B 97 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY C 96 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS B 99 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 98 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 85 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 85 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.483A pdb=" N GLY C 103 " --> pdb=" O GLY B 104 " (cutoff:3.500A) 83 hydrogen bonds defined for protein. 249 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: 1.60 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2615 1.03 - 1.23: 5 1.23 - 1.42: 1375 1.42 - 1.62: 1575 1.62 - 1.82: 20 Bond restraints: 5590 Sorted by residual: bond pdb=" CA GLY E 104 " pdb=" C GLY E 104 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 8.68e-01 bond pdb=" CA GLY B 104 " pdb=" C GLY B 104 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.76e-01 bond pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.19e-01 bond pdb=" CG TYR B 33 " pdb=" CD1 TYR B 33 " ideal model delta sigma weight residual 1.389 1.375 0.014 2.10e-02 2.27e+03 4.26e-01 bond pdb=" CA THR B 17 " pdb=" HA THR B 17 " ideal model delta sigma weight residual 0.970 0.958 0.012 2.00e-02 2.50e+03 3.54e-01 ... (remaining 5585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9595 1.63 - 3.25: 278 3.25 - 4.88: 47 4.88 - 6.51: 0 6.51 - 8.14: 15 Bond angle restraints: 9935 Sorted by residual: angle pdb=" N ASN E 97 " pdb=" CA ASN E 97 " pdb=" C ASN E 97 " ideal model delta sigma weight residual 107.62 100.11 7.51 1.97e+00 2.58e-01 1.45e+01 angle pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" C ASN A 97 " ideal model delta sigma weight residual 107.62 100.18 7.44 1.97e+00 2.58e-01 1.43e+01 angle pdb=" N ASN B 97 " pdb=" CA ASN B 97 " pdb=" C ASN B 97 " ideal model delta sigma weight residual 107.62 100.24 7.38 1.97e+00 2.58e-01 1.40e+01 angle pdb=" N ASN D 97 " pdb=" CA ASN D 97 " pdb=" C ASN D 97 " ideal model delta sigma weight residual 107.62 100.25 7.37 1.97e+00 2.58e-01 1.40e+01 angle pdb=" N ASN C 97 " pdb=" CA ASN C 97 " pdb=" C ASN C 97 " ideal model delta sigma weight residual 107.62 100.27 7.35 1.97e+00 2.58e-01 1.39e+01 ... (remaining 9930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 2400 13.51 - 27.01: 205 27.01 - 40.52: 75 40.52 - 54.02: 32 54.02 - 67.53: 28 Dihedral angle restraints: 2740 sinusoidal: 1385 harmonic: 1355 Sorted by residual: dihedral pdb=" CA GLY D 15 " pdb=" C GLY D 15 " pdb=" N LYS D 16 " pdb=" CA LYS D 16 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLY E 15 " pdb=" C GLY E 15 " pdb=" N LYS E 16 " pdb=" CA LYS E 16 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLY B 15 " pdb=" C GLY B 15 " pdb=" N LYS B 16 " pdb=" CA LYS B 16 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 2737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 202 0.032 - 0.063: 110 0.063 - 0.095: 72 0.095 - 0.127: 32 0.127 - 0.158: 19 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE E 20 " pdb=" N ILE E 20 " pdb=" C ILE E 20 " pdb=" CB ILE E 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE D 20 " pdb=" N ILE D 20 " pdb=" C ILE D 20 " pdb=" CB ILE D 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 432 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 102 " -0.001 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" CG PHE C 102 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 102 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 102 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 102 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 102 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE C 102 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE C 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE C 102 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE C 102 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 102 " -0.001 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" CG PHE B 102 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE B 102 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 102 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE B 102 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE B 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE B 102 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE B 102 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 102 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 102 " 0.000 2.00e-02 2.50e+03 2.21e-02 1.47e+01 pdb=" CG PHE A 102 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 102 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 102 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 102 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 102 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE A 102 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 PHE A 102 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 102 " 0.009 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 144 2.11 - 2.73: 9149 2.73 - 3.35: 13555 3.35 - 3.98: 18395 3.98 - 4.60: 27655 Nonbonded interactions: 68898 Sorted by model distance: nonbonded pdb=" OD1 ASN A 1 " pdb=" HG SER B 26 " model vdw 1.485 2.450 nonbonded pdb=" HG SER C 26 " pdb=" OD1 ASN B 1 " model vdw 1.493 2.450 nonbonded pdb=" OD1 ASN C 1 " pdb=" HG SER D 26 " model vdw 1.500 2.450 nonbonded pdb=" OD1 ASN D 1 " pdb=" HG SER E 26 " model vdw 1.501 2.450 nonbonded pdb=" OE1 GLN B 92 " pdb=" HH TYR B 94 " model vdw 1.526 2.450 ... (remaining 68893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.120 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.190 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2975 Z= 0.171 Angle : 0.932 8.136 4040 Z= 0.532 Chirality : 0.059 0.158 435 Planarity : 0.005 0.023 515 Dihedral : 12.165 49.684 990 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.28), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP A 36 HIS 0.014 0.004 HIS B 32 PHE 0.044 0.010 PHE C 102 TYR 0.047 0.007 TYR D 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.420 Fit side-chains REVERT: D 35 GLN cc_start: 0.7436 (pt0) cc_final: 0.7187 (pm20) REVERT: E 68 ASP cc_start: 0.7589 (t0) cc_final: 0.7320 (t0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1606 time to fit residues: 12.8932 Evaluate side-chains 25 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2975 Z= 0.274 Angle : 0.625 4.474 4040 Z= 0.350 Chirality : 0.049 0.129 435 Planarity : 0.004 0.025 515 Dihedral : 7.954 24.071 400 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.52 % Allowed : 11.21 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 36 HIS 0.003 0.001 HIS A 99 PHE 0.011 0.002 PHE E 2 TYR 0.011 0.002 TYR B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.482 Fit side-chains REVERT: E 35 GLN cc_start: 0.7884 (pt0) cc_final: 0.7604 (mm-40) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.1598 time to fit residues: 7.4929 Evaluate side-chains 26 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2975 Z= 0.301 Angle : 0.634 4.413 4040 Z= 0.355 Chirality : 0.049 0.142 435 Planarity : 0.004 0.033 515 Dihedral : 7.874 23.410 400 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.03 % Allowed : 16.06 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.28), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 100 HIS 0.003 0.001 HIS A 99 PHE 0.019 0.003 PHE B 102 TYR 0.011 0.002 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: E 35 GLN cc_start: 0.7939 (pt0) cc_final: 0.7605 (mm-40) outliers start: 10 outliers final: 5 residues processed: 31 average time/residue: 0.1565 time to fit residues: 6.9603 Evaluate side-chains 27 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2975 Z= 0.237 Angle : 0.602 5.054 4040 Z= 0.332 Chirality : 0.048 0.128 435 Planarity : 0.004 0.032 515 Dihedral : 7.369 22.780 400 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.73 % Allowed : 16.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 36 HIS 0.002 0.001 HIS A 99 PHE 0.010 0.002 PHE A 102 TYR 0.007 0.001 TYR D 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.476 Fit side-chains REVERT: E 35 GLN cc_start: 0.7895 (pt0) cc_final: 0.7613 (mm-40) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 0.1754 time to fit residues: 7.2404 Evaluate side-chains 28 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2975 Z= 0.330 Angle : 0.652 5.288 4040 Z= 0.365 Chirality : 0.048 0.145 435 Planarity : 0.004 0.036 515 Dihedral : 7.662 24.361 400 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 4.55 % Allowed : 16.67 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 100 HIS 0.008 0.001 HIS B 32 PHE 0.012 0.003 PHE B 102 TYR 0.010 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7389 (tt0) REVERT: E 2 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7270 (t80) REVERT: E 35 GLN cc_start: 0.7987 (pt0) cc_final: 0.7682 (mm-40) outliers start: 15 outliers final: 9 residues processed: 36 average time/residue: 0.1577 time to fit residues: 8.0566 Evaluate side-chains 34 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 2 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2975 Z= 0.153 Angle : 0.579 5.927 4040 Z= 0.314 Chirality : 0.048 0.132 435 Planarity : 0.003 0.028 515 Dihedral : 6.835 21.276 400 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.73 % Allowed : 19.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 36 HIS 0.003 0.001 HIS D 32 PHE 0.008 0.001 PHE B 102 TYR 0.006 0.001 TYR B 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7529 (mtt) cc_final: 0.7246 (mtt) REVERT: E 35 GLN cc_start: 0.7929 (pt0) cc_final: 0.7659 (mm-40) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1653 time to fit residues: 8.1746 Evaluate side-chains 30 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2975 Z= 0.228 Angle : 0.599 5.740 4040 Z= 0.326 Chirality : 0.047 0.130 435 Planarity : 0.004 0.032 515 Dihedral : 6.917 22.095 400 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 3.94 % Allowed : 19.39 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 36 HIS 0.005 0.001 HIS B 32 PHE 0.010 0.002 PHE B 102 TYR 0.007 0.001 TYR B 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 22 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.7532 (mtt) cc_final: 0.7199 (mtt) REVERT: B 32 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7562 (m90) REVERT: E 35 GLN cc_start: 0.7982 (pt0) cc_final: 0.7668 (mm-40) outliers start: 13 outliers final: 8 residues processed: 31 average time/residue: 0.1615 time to fit residues: 7.1920 Evaluate side-chains 31 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2975 Z= 0.133 Angle : 0.565 5.952 4040 Z= 0.306 Chirality : 0.047 0.132 435 Planarity : 0.003 0.030 515 Dihedral : 6.508 20.097 400 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.82 % Allowed : 21.52 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 36 HIS 0.005 0.001 HIS B 32 PHE 0.008 0.001 PHE E 102 TYR 0.007 0.001 TYR E 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.7599 (mtt) cc_final: 0.7233 (mtt) REVERT: E 35 GLN cc_start: 0.7939 (pt0) cc_final: 0.7667 (mm-40) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1673 time to fit residues: 6.5389 Evaluate side-chains 29 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2975 Z= 0.131 Angle : 0.555 5.794 4040 Z= 0.300 Chirality : 0.047 0.127 435 Planarity : 0.003 0.030 515 Dihedral : 6.319 19.874 400 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.12 % Allowed : 21.21 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 36 HIS 0.015 0.001 HIS A 32 PHE 0.009 0.001 PHE E 102 TYR 0.009 0.001 TYR A 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.7602 (mtt) cc_final: 0.7224 (mtt) REVERT: E 35 GLN cc_start: 0.7947 (pt0) cc_final: 0.7674 (mm-40) outliers start: 7 outliers final: 7 residues processed: 28 average time/residue: 0.1648 time to fit residues: 6.6575 Evaluate side-chains 29 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 28 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2975 Z= 0.106 Angle : 0.545 5.963 4040 Z= 0.293 Chirality : 0.047 0.129 435 Planarity : 0.003 0.029 515 Dihedral : 6.082 19.070 400 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.52 % Allowed : 21.82 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 36 HIS 0.012 0.001 HIS A 32 PHE 0.011 0.001 PHE E 102 TYR 0.008 0.001 TYR B 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.7498 (mtt) cc_final: 0.7098 (mtt) REVERT: E 35 GLN cc_start: 0.7911 (pt0) cc_final: 0.7662 (mm-40) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.1738 time to fit residues: 6.3270 Evaluate side-chains 25 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 102 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.084892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.074469 restraints weight = 20931.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.076974 restraints weight = 8862.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.078679 restraints weight = 4800.968| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2975 Z= 0.127 Angle : 0.536 5.992 4040 Z= 0.289 Chirality : 0.047 0.125 435 Planarity : 0.004 0.030 515 Dihedral : 5.921 18.653 400 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 1.82 % Allowed : 21.82 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 36 HIS 0.003 0.001 HIS D 32 PHE 0.010 0.001 PHE E 102 TYR 0.004 0.001 TYR D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.00 seconds wall clock time: 39 minutes 13.19 seconds (2353.19 seconds total)